release: plyngent 0.6.0

Appending via edit_lineno required the last line to be read, which made
writing to an empty file impossible (line 0 does not exist). An empty
file has nothing to clobber, so the append needs no prior read.

.gitignore

@@ -214,3 +214,6 @@ __marimo__/
 
 # Streamlit
 .streamlit/secrets.toml
+
+# codegraph (local code index)
+.codegraph/

AGENTS.md

@@ -1,4 +1,4 @@
-# CLAUDE.md
+# AGENTS.md
 
 This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 
@@ -56,15 +56,17 @@ lmproto/deepseek/anthropic/     ← DeepSeek Anthropic client (extends Anthropic
 
 ### Config (`config/`)
 
-TOML load/store (`ConfigStore`): `[providers]` tagged union presets, `[database]` section. Default path via platformdirs. Providers may set `timeout` as a float or `{ connect, read }` (`HttpTimeoutConfig`); omitted → product defaults (10s connect / 600s read). `DeepseekProvider.convention` (Literal: `""`/`"openai"`/`"anthropic"`/`"responses"`) selects the DeepSeek API surface — `"responses"` → OpenAI Responses, `"anthropic"` → Anthropic Messages on `https://api.deepseek.com/anthropic` (default url follows the convention); a per-model `ModelConfig.convention` overrides it (empty = inherit).
+TOML load/store (`ConfigStore`): `[providers]` tagged union presets, `[database]` section. Default path via platformdirs. Providers may set `timeout` as a float or `{ connect, read }` (`HttpTimeoutConfig`); omitted → product defaults (10s connect / 600s read). `DeepseekProvider.convention` (Literal: `""`/`"openai"`/`"anthropic"`/`"responses"`) selects the DeepSeek API surface — `"responses"` → OpenAI Responses, `"anthropic"` → Anthropic Messages on `https://api.deepseek.com/anthropic` (default url follows the convention); a per-model `ModelConfig.convention` overrides it (empty = inherit). `[mcp]` (`McpConfig`): `servers.<name>` stdio server definitions (`McpServerConfig`: `command`/`args`/`env`/`cwd`/`timeout`/`read_only`, `url` reserved for streamable HTTP) + `disable` gate; defining a server opts it in.
 
 ### Runtime (`runtime/`)
 
 `create_client(provider)` maps config `Provider` → protocol client by effective preset (model-level `preset`/`url` overrides apply). `normalize_http_timeout` feeds OpenAI-compatible configs and Anthropic. Mapping: `openai` → `OpenAIClient` (agent uses Responses), `openai-compatible` / `deepseek` → chat-completions clients (deepseek with effective `convention = "responses"` → `DeepseekResponsesClient`, `"anthropic"` → `DeepseekAnthropicClient`), `anthropic` → `AnthropicClient`.
 
+MCP (`runtime/mcp_client.py`): `McpManager` owns one `McpServerConnection` per `[mcp]` server — a spawned stdio subprocess speaking newline-delimited JSON-RPC 2.0: initialize handshake, `tools/list` (cursor pagination), `tools/call`, `notifications/tools/list_changed` → `tools_stale`. Spawn/handshake failures record `connection.error` (status string), never raise; `ensure_started` / `restart(config)` / `aclose` / `refresh_tools`; `statuses()` → `(server, status, tool_count)` rows; `instructions()` → `(server, text)` for every connected server that returned optional `InitializeResult.instructions` (usage guidance captured per connection); per-request timeout from config (default 30s).
+
 ### Memory (`memory/`)
 
-Async SQLAlchemy + aiosqlite. `MemoryStore`: schema init (+ lightweight SQLite `ALTER` for new columns), default local user, sessions (bound to `workspace` path; optional `provider_name`/`model`), messages stored as msgspec chat message JSON.
+Async SQLAlchemy + aiosqlite. `MemoryStore`: schema init (+ lightweight SQLite `ALTER` for new columns; `PRAGMA user_version` 4), default local user, sessions (bound to `workspace` path; optional `provider_name`/`model`; `todo_stack` + `access_grants` JSON columns), messages stored as msgspec chat message JSON.
 
 ### Agent (`agent/`)
 
@@ -78,23 +80,25 @@ Async SQLAlchemy + aiosqlite. `MemoryStore`: schema init (+ lightweight SQLite `
 - **`/compact`**: soft-compact tool dumps → model summary (no tools) via the same kind dispatch → **new** session seeded with summary message. Soft-compact keeps the last **12** tool results full-size by default (`DEFAULT_RECENT_TOOL_RESULTS`); older tool payloads shrink first.
 - Events: text_delta, **reasoning_delta**, assistant_message, tool_call/result, max_rounds, **error** (`retryable`/`source`), **cancelled** (`reason`), **usage** (`TokenUsage`).
 - Usage: API `usage` from completions (stream with `include_usage`); **char≈token fallback** (~4 chars/token) when omitted; **context size** = last request ``prompt_tokens`` (API preferred); `last_turn_usage` / `session_usage` are **billed sums** (tool rounds re-send history); CLI end-of-turn + `/status`.
-- Config ``[agent]``: `system_prompt` (persona; default `DEFAULT_SYSTEM_PROMPT`; `""` omits persona), `tool_directives` (tool playbook; default `DEFAULT_TOOL_DIRECTIVES`; `""` omits playbook; both empty → no system), `max_tool_result_chars`, `parallel_tools`, `confirm_destructive`, `path_denylist`, `max_context_tokens` (default 200k est. tokens). Truncated tool results carry a model hint (`[Truncated (N chars max; M omitted). You may ask for user to increase the limit via configuration file.]`) so the model can ask the user to raise `max_tool_result_chars`; request-time compact shrinks (`hint=False`) keep the terse `...[truncated N characters]` marker.
+- Config ``[agent]``: `system_prompt` (persona; default `DEFAULT_SYSTEM_PROMPT`; `""` omits persona), `tool_directives` (tool playbook; default `DEFAULT_TOOL_DIRECTIVES`; `""` omits playbook; both empty → no system), `mcp_instructions` (fold connected MCP servers' initialize ``instructions`` into the system prompt when tools on; default true), `allow_paths` (static out-of-workspace pre-allow `path → read|write|exec`; never prompts), `auto_continue_limits` (auto-raise tool/PTY limits without prompting; default false), `max_tool_result_chars`, `parallel_tools`, `confirm_destructive`, `path_denylist`, `max_context_tokens` (default 200k est. tokens). Truncated tool results carry a model hint (`[Truncated (N chars max; M omitted). You may ask for user to increase the limit via configuration file.]`) so the model can ask the user to raise `max_tool_result_chars`; request-time compact shrinks (`hint=False`) keep the terse `...[truncated N characters]` marker.
 
 ### Tools (`tools/`)
 
 Module-level `@tool` handlers. Call `set_workspace_root()` before use.
 
-- **`workspace`**: path resolve under primary root **or** temporary allowlist roots; path substring denylist; command basename denylist (CLI: timed human allow override, default deny on timeout; **not** skipped by YOLO); clearer deny messages.
-- **`file`**: `read_file` (`with_lineno`, `max_chars` default 32k; results start with a 1-based `L{begin}-{end}` range), `write_file`, `listdir`, `tree` (VCS + default noise dirs + optional `skip_dirs` / denylist walk), `glob_paths`, `grep_files` (regex, skip VCS/binary), `edit_replace` (`max_replaces`, reports remaining matches), `edit_lineno` (1-based range; only lines read via `with_lineno`; read state resets on any file write/edit/copy/move/delete), `copy_path` / `move_path` / `delete_path`, `new_temporary_workspace` (system temp allowlist; cleanup on chat exit; no session rebind), `get_truncated` (resume any truncated result via its `truncate_token=...`).
+- **`workspace`**: path resolve under primary root **or** temporary allowlist roots **or** a directory-access grant (mode-aware: `read` < `write` < `exec`, default required `write`; a file grant matches only that file); path substring denylist (wins over grants); command basename denylist (CLI: timed human allow override, default deny on timeout; **not** skipped by YOLO); escape error hints `request_directory_access`.
+- **`access`** (`tools/access.py`): `request_directory_access` (LOCAL|INSTANCE|SESSION) asks the host hook for out-of-workspace access; grants are one `path → mode` pair in one of three stores — `WorkspacePolicy.config_allow` (static `[agent].allow_paths`), `SessionState.access_grants` (human-approved, persisted on the session row), `WorkspacePolicy.yolo_allow` (`--yes`/`/yolo`, process only). `AccessDecision(mode, persist)` from the hook; denylisted paths can never be granted; cap `MAX_ACCESS_GRANTS`. Not a sandbox: `exec` grants (and any command) reach the whole FS.
+- **`file`**: `read_file` (`with_lineno`, `max_chars` default 32k; results start with a 1-based `L{begin}-{end}` range), `write_file`, `listdir`, `tree` (model picks `format=markdown` default / `flat` paths / `decorated`; VCS + default noise dirs + optional `skip_dirs` / denylist walk), `glob_paths`, `grep_files` (regex, skip VCS/binary), `edit_replace` (`max_replaces`, reports remaining matches), `edit_lineno` (1-based range; only lines read via `with_lineno`; read state resets on any file write/edit/copy/move/delete), `copy_path` / `move_path` / `delete_path`, `new_temporary_workspace` (system temp allowlist; cleanup on chat exit; no session rebind), `get_truncated` (resume any truncated result via its `truncate_token=...`).
 - **`process`**: `run_argv` (argv, no shell, timeout, optional stdin/env); `run_argv_batch` (serial steps, `pipe_out` on provider, `mix_stderr`, `stop_on_error`); PTY `open_pty` / `read_pty` / `write_pty` (literal) / `write_pty_keys` (escapes) / `ask_into_pty` (human→PTY only; `secret` no-echo; answer never in tool result) / `close_pty` (POSIX: `pty`+`fork`; Windows: ConPTY via `pywinpty` env marker dep).
 - PTY: backend in `pty_backend.py`; structured status (`alive`/`exit_code`/`data`); `read_pty(..., until=)` (**CSI sanitized** so host TTY is never reset); keys via `write_pty_keys` only (`\xHH`, `ctrl+x`, `key=esc`); secrets via `ask_into_pty` (not `write_pty` data); session limit/idle TTL/output budget; close terminate→kill.
-- CLI limit hooks: interactive confirm to raise tool-loop rounds, PTY session cap, or PTY output budget.
+- CLI limit hooks: interactive confirm to raise tool-loop rounds, PTY session cap, or PTY output budget. The prompt accepts `y`/empty (once), `n`, or `yyy` = stop asking for the rest of the turn (`cli.limits` module flag, reset by `run_turn_with_retries`, `/btw`, session switches, and chat exit). `--auto-continue` / `[agent] auto_continue_limits` set the process-wide default (covers one-shot/PTY); the flag does not imply YOLO and vice versa.
 - Destructive confirms: `classify_danger` + `ToolRegistry(on_confirm=…)`; CLI default deny; config `confirm_destructive` / `path_denylist`. Soft confirm also for shells/REPLs and `python|bash -c` one-liners (argv + code preview); deny may include a user comment for the model. Session YOLO: `/yolo on|off|once` and `--yes` (skip soft confirms; hard denylists unchanged; `once` expires after the next user turn).
 - **`vcs`**: read-only VCS tools (`vcs_kind` / `vcs_status` / `vcs_diff` / `vcs_log` / `vcs_branch`) via `VcsBackend` protocol; **git** implemented; detectors are pluggable for other systems.
 - **`chat`**: human prompts as tools — `ask_user_line` / `ask_user_choice` / `ask_user_form` (shared `prompting` core); `wait` (line prompt with timeout; Enter disturbs).
 - **`todo`**: LIFO stack of **task groups** (not a queue of tasks) — `todo_push` creates one group of siblings; `todo_pop` removes the whole top group; `todo_update` by id; DFS breakdown push[T1,T2]→push[T1.1…]→pop→push[T2.1…]; stored on session row; open items = unfinished work (`[TODO OPEN WORK]`); all-terminal non-empty = hygiene (`[TODO HYGIENE]`); nag channel via `[agent] todo_nag_strategy` (`developer`/`user` = prose nag; `synthetic_tool` = forged `todo_list` call + **real** `stack.render()` result + ToolCall/Result events; `none`).
 - **`net` / `fetch`**: HTTP GET/POST/PUT/DELETE via niquests (isolated session, not the LLM client). Manual redirects with per-hop SSRF checks (`asyncio` `getaddrinfo`). Private/loopback hosts need instance policy grant (CLI timed confirm; **not** YOLO). Public cleartext HTTP and mutating methods soft-confirm (`YOLO`/`TRUSTABLE`). HTTPS→HTTP redirects blocked unless `allow_http_downgrade`. `user_agent` tool arg (or headers) is never replaced by the default when provided. Caps: body bytes/chars, request body size.
-- **`DEFAULT_TOOLS` / catalog**: file + process + vcs + chat + todo + net (`fetch`) for local surface.
+- **`mcp`** (`tools/mcp.py`): register one server's advertised tools into the catalog as namespaced `mcp__<server>__<tool>` definitions with `ToolSource(kind="mcp", plugin_id=server)`; tags LOCAL (+ READ_ONLY when the server config sets `read_only`) — never YOLO/TRUSTABLE. `register_mcp_tools` purges prior MCP entries then re-registers every connected server (hosts call it on tool-registry rebuild); connections must already be started by `McpManager`.
+- **`DEFAULT_TOOLS` / catalog**: access + file + process + vcs + chat + todo + net (`fetch`) for local surface. `ToolTag.READ_ONLY` marks non-mutating tools (`read_file`, `get_truncated`, `listdir`, `glob_paths`, `grep_files`, `tree`, `todo_list`, `wait`, `ask_user_*`, `vcs_*`, `fetch`); `ToolRegistry.clone(read_only_only=True)` selects just those for safe side turns / planning, and `read_only_context()` (in `tools/context.py`) makes `fetch` accept GET only.
 
 ### Prompting (`prompting.py`)
 
@@ -104,8 +108,9 @@ Shared interactive I/O: `ask` / `choose` / `form` / `confirm` with pluggable bac
 
 Click app + readline REPL. Entry: `plyngent` / `python -m plyngent`.
 
-- **`plyngent chat`**: provider/model (flags or interactive; Tab via readline in `prompting`); sessions store `provider_name`/`model` and restore on resume; SQLite via `[database]` (file DB under user data when url unset; explicit `url = ":memory:"` kept + warn); workspace-bound; resume latest for cwd/`--workspace` by default (`--new` / `--session`). One-shot: `-p/--prompt` and non-TTY stdin; exit codes 0/1/2/3; `--yes` (YOLO on), `--stream/--no-stream`, `--quiet`. Root `--log-level`.
-- Slash: Click group in `cli/slash.py` + `awaitlet` for async work; Tab completer from registry + ParamType `shell_complete`. Multiline `"""` … `"""`; `/edit` via `$VISUAL`/`$EDITOR` (blocking only). `/yolo on|off|once` for soft destructive confirms. `/model --persist` / `/models --persist` write model catalog entries into TOML. `/todos` for human show/push/pop/clear of the todo stack.
+- **`plyngent chat`**: provider/model (flags or interactive; Tab via readline in `prompting`); sessions store `provider_name`/`model` and restore on resume; SQLite via `[database]` (file DB under user data when url unset; explicit `url = ":memory:"` kept + warn); workspace-bound; resume latest for cwd/`--workspace` by default (`--new` / `--session`). One-shot: `-p/--prompt` and non-TTY stdin; exit codes 0/1/2/3; `--yes` (YOLO on), `--auto-continue` (auto-raise limits), `--stream/--no-stream`, `--quiet`. Root `--log-level`. Enabled `[mcp]` servers start before the REPL (`_start_mcp_manager`, per-server failures warn on stderr) and are closed on exit (`McpManager.aclose`).
+- Slash: Click group in `cli/slash.py` + `awaitlet` for async work; Tab completer from registry + ParamType `shell_complete`. Multiline `"""` … `"""`; `/edit` via `$VISUAL`/`$EDITOR` (blocking only). `/yolo on|off|once` for soft destructive confirms. `/model --persist` / `/models --persist` write model catalog entries into TOML. `/todos` for human show/push/pop/clear of the todo stack. `/mcp` (`list` default) prints per-server status/tool counts + an `instructions` preview when the server sent usage guidance, + last stderr lines; `/mcp reconnect` re-reads config, restarts every enabled server, and rebuilds the tool registry. `/grants` lists directory-access grants (`revoke <index|all>`; config grants point at the TOML); `/status` includes the grant count.
+- `/btw` side questions: forked session; main transcript/DB untouched. `--tools=read` (default) exposes only `READ_ONLY` tools under `read_only_context()` (fetch=GET) with the main session view; `--tools=no` off; `--tools=full` whole-registry clone with fresh session. Tools off: default falls back to no tools; explicit `read`/`full` errors.
 - Explicit `/resume` or `--session` from another workspace prompts: **keep** / **update** / **abort**.
 - Failed/cancelled turns: user kept; **committed tool rounds kept** (side effects not re-run on `/retry`); only unfinished assistant rolled back; Ctrl+C cancels; TTY confirms off-loop; auto-retry 10s/20s/30s then `/retry`.
 - **`plyngent providers`**, **`config path|edit`**. Config open: `$VISUAL`/`$EDITOR` (wait), else system default (`xdg-open` / `open` / `startfile`, non-blocking). `/edit` stays blocking-only. No providers → optional edit then reload when waited.
@@ -135,7 +140,7 @@ Basedpyright `recommended`. Ruff includes `ANN` (private return types `ANN202` i
   - G3: multiline `"""` … `"""` input (`cli/input_text.py`); `/edit` via `$EDITOR` (`edit_text_in_editor`)
   - G4: `plyngent chat -p/--prompt` (+ non-TTY stdin); exit codes 0/1/2/3; `--yes` / non-interactive confirm deny; `--stream/--no-stream`, `--quiet`
   - G5: PTY master FD non-inheritable; `read_pty`/`close_pty` via `to_thread`; `PtyManager.close_all()` on chat exit; `--log-level`; clearer invalid TOML errors; export/status stay secret-free
-  - G6: README, `doc/plyngent.example.toml`, CLAUDE overview/CLI notes
+  - G6: README, `doc/plyngent.example.toml`, AGENTS overview/CLI notes
 
   Phase G complete for single-user CLI polish. Next roadmap work is Phase H or optional F (cost/tokenizer).
 

README.md

@@ -147,6 +147,13 @@ access_key_or_token = "sk-..."
 # tool_directives = '''### Workspace ...'''
 confirm_destructive = true
 max_context_tokens = 200000
+# Fold MCP server initialize ``instructions`` (usage guidance) into the
+# system prompt when tools are on (default true; false ignores server text).
+# mcp_instructions = true
+# Static out-of-workspace pre-allow (path → read|write|exec); never prompts.
+# allow_paths = { "/data/datasets" = "read", "/tmp/build" = "exec" }
+# Auto-raise tool/PTY limits without prompting (same as answering yyy).
+# auto_continue_limits = false
 
 # Optional plugins (entry-point names); default load none. See doc/plugins.md.
 # [plugins]
@@ -157,6 +164,8 @@ Per-provider **`timeout`** is passed to the HTTP session for chat/completions, R
 
 Third-party **plugins**: install a package that declares `project.entry-points."plyngent.tools"` (and later other groups), then allowlist the entry-point name under **`[plugins].enable`**. Details: [doc/plugins.md](doc/plugins.md).
 
+**MCP servers** (Model Context Protocol over stdio): define servers under `[mcp.servers.<name>]` (`command` + `args`, optional `env`/`cwd`/`timeout`/`read_only`) and their tools become agent tools namespaced `mcp__<server>__<tool>` (LOCAL tags; `read_only = true` also marks them READ_ONLY, eligible for `/btw --tools=read`). Names in `[mcp].disable` stay disconnected. A server may also return optional `instructions` (usage guidance) in its MCP `initialize` response; when tools are on those are folded into the agent system prompt as `MCP server <name> instructions:` blocks (`[agent] mcp_instructions = false` disables), and `/mcp` previews them. In the REPL, `/mcp` lists per-server status and tool counts; `/mcp reconnect` re-reads the config file and restarts every enabled server (adopts newly added ones).
+
 Supported provider presets today:
 
 | Preset | API used by the agent | Notes |
@@ -209,10 +218,13 @@ plyngent chat --session 3
 | `--stream` / `--no-stream` | Streaming deltas (default on) |
 | `--quiet` | Less status on stderr |
 | `--yes` | YOLO on: skip destructive-tool confirms for this process |
+| `--auto-continue` | Auto-raise tool/PTY limits without prompting (like answering `yyy`) |
 | `--log-level` | On the root CLI: `DEBUG`, `INFO`, `WARNING`, … |
 
 Sessions resume the **most recently updated** session for the current workspace unless you pass `--new` or `--session`. Each session remembers the last **provider** and **model** (restored on resume so you are not re-prompted).
 
+When a tool-loop or PTY limit is hit, the prompt accepts `y` (continue once), `n` (stop), or `yyy` — **stop asking for the rest of this turn** (the next user turn prompts again). `--auto-continue` / `[agent] auto_continue_limits = true` skip the prompt for every turn.
+
 ### One-shot (scripts / CI)
 
 ```bash
@@ -252,11 +264,13 @@ Type `/help` in the REPL for the live list. Common ones:
 | `/yolo [on\|off\|once]` | Soft destructive confirms: sticky skip, off, or next turn only |
 
 | `/retry` | Re-run incomplete last user turn (after error/cancel) |
+| `/btw [--tools read\|no\|full] [--fresh]` | Side question without changing the main session (read-only tools by default) |
 | `/provider` `/model` | Switch without restarting |
 | `/model --persist` | Save current model id into `plyngent.toml` catalog |
 | `/models` | List config + remote `GET /models` (always re-fetches) |
 | `/models --persist` | Merge remote catalog into TOML for this provider |
 | `/todos` | Todo/task stack: list, push, pop, done, clear |
+| `/grants` | Directory-access grants: list, or `revoke <index\|all>` |
 | `/config` | Edit `plyngent.toml` ($VISUAL/$EDITOR or system open); reload after blocking editor |
 | `/quit` | Leave the REPL |
 
@@ -266,15 +280,16 @@ User messages are saved immediately. On API error or Ctrl+C, partial assistant/t
 
 - **Workspace** = root for file/process/VCS tools (default cwd).
 - **Session** = SQLite chat bound to a workspace path.
+- Paths outside the workspace need a **directory-access grant**: the model calls `request_directory_access` (`read` / `write` / `exec`), the human approves at the requested level or another one (timed y/N, default deny; `--yes`/`/yolo` auto-approve as a process-only grant), and approval lasts for the session (`/grants` lists/revokes). Static pre-allow lives under `[agent].allow_paths`. The path denylist always wins, and grants gate path-resolving tools only — they are **not** a sandbox (`run_argv`/PTY reach the whole filesystem).
 - Resuming a session from another directory prompts: keep session workspace, rebind to current, or abort.
 
 ## Tools (when enabled)
 
-Default registry: file ops (including `tree` with default noise-dir skips), `run_argv` / `run_argv_batch` / PTY (POSIX openpty; Windows ConPTY via pywinpty), read-only VCS (git), HTTP `fetch` (GET/POST/PUT/DELETE via niquests; private/loopback hosts need a human policy grant, not YOLO), human prompts (`ask_user_line` / `ask_user_choice` / `ask_user_form`), `wait` (line prompt with timeout; Enter disturbs), `get_truncated` (resume any truncated result via its `truncate_token=...`), and todo stack tools (`todo_list` / `todo_push` / `todo_pop` / `todo_update` / `todo_clear`).
+Default registry: file ops (including `tree` with a markdown bullet-list default, `flat` paths or classic `decorated` on demand; default noise-dir skips), `run_argv` / `run_argv_batch` / PTY (POSIX openpty; Windows ConPTY via pywinpty), read-only VCS (git), HTTP `fetch` (GET/POST/PUT/DELETE via niquests; private/loopback hosts need a human policy grant, not YOLO), human prompts (`ask_user_line` / `ask_user_choice` / `ask_user_form`), `wait` (line prompt with timeout; Enter disturbs), `request_directory_access` (out-of-workspace access grants), `get_truncated` (resume any truncated result via its `truncate_token=...`), and todo stack tools (`todo_list` / `todo_push` / `todo_pop` / `todo_update` / `todo_clear`).
 
 Safety defaults:
 
-- Paths stay under the workspace; optional `path_denylist` substrings (`tree` also skips denylisted children by default).
+- Paths stay under the workspace unless granted (`request_directory_access` / `[agent].allow_paths`); optional `path_denylist` substrings always apply (`tree` also skips denylisted children by default).
 - Command basename denylist (e.g. dangerous shells/utilities).
 - Destructive tools (delete/move/overwrite) can require confirm (`confirm_destructive`; default deny in non-TTY). Override for the session with `/yolo on|off|once` or startup `--yes` (path/command denylists still apply).
 - PTY sessions: caps, idle TTL, output budget; master FD is non-inheritable; sessions closed on chat exit.
@@ -299,7 +314,7 @@ plyngent --log-level INFO chat ...
 
 ## Architecture (short)
 
-See [doc/architecture.md](doc/architecture.md) and [CLAUDE.md](CLAUDE.md) for developers.
+See [doc/architecture.md](doc/architecture.md) and [AGENTS.md](AGENTS.md) for developers.
 
 - **`lmproto/`** — OpenAI-compatible, OpenAI Responses, Anthropic Messages, DeepSeek msgspec models and async SSE clients  
 - **`agent/`** — kind-based tool loop (`chat_completions` / `responses` / `messages`), streaming, usage, compact  

doc/architecture.md

@@ -27,8 +27,8 @@
     - agent: Kind-based tool loop, streaming, usage, compact; bridges:
       ``responses_bridge``/``responses_dispatch``, ``messages_bridge``/``messages_dispatch``;
       ``@tool`` / tags / registry. History stays chat-completions-shaped.
-    - tools: Workspace file/process/VCS/chat/todo/net tools; catalog; plugins;
-      instance/session context and views.
+    - tools: Workspace file/process/VCS/chat/todo/net tools + directory-access
+      grants (`access`); catalog; plugins; instance/session context and views.
     - prompting: Shared ask/choose/form for CLI and tools.
     - cli: Click entry, slash registry, REPL, one-shot chat.
     - web: Web service (Phase H; not implemented).

doc/plugins.md

@@ -50,6 +50,11 @@ Notes:
 - Optional soft-confirm bits: **`YOLO`** (eligible for YOLO auto-approve),
   **`TRUSTABLE`** (grant once per session after approve). Hard denylists are
   never YOLO-skipped.
+- Optional host-policy bit: **`READ_ONLY`** marks tools that never mutate host
+  state — they become eligible for read-only contexts such as
+  `/btw --tools=read` side turns or planning. Tools that only sometimes mutate
+  (e.g. `fetch` with a non-GET method) may still opt in; the handler must
+  enforce the constraint via the read-only context flag.
 - Docstring becomes the model-facing description; parameter schemas come from
   type hints.
 - Use `register=False` only for unit tests that build a private registry.

doc/plyngent.example.toml

@@ -26,6 +26,22 @@
 # [networking]
 # ssrf_assume_public_cidrs = ["198.18.0.0/15"]
 
+# MCP (Model Context Protocol) servers exposed as agent tools.
+# Defining a server opts it in; tools appear as mcp__<server>__<tool> with
+# LOCAL tags (confirm flow applies). Names in disable stay disconnected.
+# A server's initialize ``instructions`` (usage guidance) is folded into the
+# agent system prompt when tools are on ([agent] mcp_instructions = false
+# disables; /mcp previews what each server sent).
+# [mcp.servers.docs]
+# command = "npx"
+# args = ["-y", "@modelcontextprotocol/server-filesystem", "/tmp"]
+# env = { RUST_LOG = "info" }
+# cwd = "/path"              # spawn working directory (empty = inherit)
+# timeout = 30.0             # per-request timeout (seconds)
+# read_only = true           # mark every tool READ_ONLY (eligible for /btw --tools=read)
+# [mcp]
+# disable = ["docs"]         # defined but never connected
+
 [agent]
 # Persona (omit → built-in coding-agent line). tool_directives is the tool playbook.
 # Override with multi-line literals (prefer ''' so nested " is fine):
@@ -42,8 +58,18 @@ max_tool_result_chars = 32000
 parallel_tools = true
 confirm_destructive = true
 path_denylist = ["/secrets/", ".ssh/", ".gnupg/"]
+# Static out-of-workspace pre-allow (path → read|write|exec); never prompts.
+# The model can also request access at runtime via request_directory_access
+# (human approves; /grants lists or revokes). Denylist still applies, and
+# grants are a tool-policy gate, not a sandbox (commands reach the FS).
+# allow_paths = { "/data/datasets" = "read", "/tmp/build" = "exec" }
+# Auto-raise tool/PTY limits without prompting (same as answering yyy).
+# auto_continue_limits = false
 # Soft context budget in estimated tokens (~4 chars/token when API usage missing).
 max_context_tokens = 200000
+# Fold connected MCP servers' initialize ``instructions`` (usage guidance)
+# into the agent system prompt when tools are on. false = ignore server text.
+# mcp_instructions = true
 # How open-todo nags are injected into model context:
 # developer (default) | user | synthetic_tool | none
 # (legacy system is treated as developer)

pdm.lock

@@ -4,7 +4,7 @@
 [metadata]
 groups = ["default", "dev"]
 strategy = ["inherit_metadata"]
-lock_version = "4.5.0"
+lock_version = "4.5.1"
 content_hash = "sha256:94dc16bf6ed12e2fcd7a109b500e9b2d7e39f224b60472d64ecb1d3436ddbb82"
 
 [[metadata.targets]]
@@ -52,53 +52,109 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.4.9"
+version = "3.5.1"
 requires_python = ">=3.7"
 summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 groups = ["default"]
 files = [
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 requires_python = ">=3.10"
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-dependencies = [
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 requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 summary = "Cross-platform colored terminal text."
-groups = ["default", "dev"]
-marker = "platform_system == \"Windows\" or sys_platform == \"win32\""
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 ]
 
 [[package]]
@@ -497,7 +553,7 @@ files = [
 
 [[package]]
 name = "sqlalchemy"
-version = "2.0.51"
+version = "2.0.52"
 requires_python = ">=3.7"
 summary = "Database Abstraction Library"
 groups = ["default"]
@@ -507,22 +563,16 @@ dependencies = [
     "typing-extensions>=4.6.0",
 ]
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 ]
 
 [[package]]
@@ -549,28 +599,28 @@ files = [
 
 [[package]]
 name = "urllib3-future"
-version = "2.24.900"
+version = "2.24.907"
 requires_python = ">=3.7"
 summary = "urllib3.future is a powerful HTTP 1.1, 2, and 3 client with both sync and async interfaces"
 groups = ["default"]
 dependencies = [
     "h11<1.0.0,>=0.11.0",
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 ]
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 ]
 
 [[package]]
 name = "wassima"
-version = "2.1.3"
+version = "2.1.4"
 requires_python = ">=3.7"
 summary = "Access your OS root certificates with utmost ease"
 groups = ["default"]
 marker = "sys_platform != \"emscripten\""
 files = [
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+    {file = "wassima-2.1.4-py3-none-any.whl", hash = "sha256:26022272d4618aada0e26df2e79dbc0e034be8be9d6d5396512690ffc6a94e7b"},
+    {file = "wassima-2.1.4.tar.gz", hash = "sha256:21bb77253bb8032c05393172c4d2df395f423b7e704538f3b2407f50c032034d"},
 ]

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "plyngent"
-version = "0.4.0"
+version = "0.6.0"
 description = "LLM chat and agent toolkit"
 authors = [
   { name = "HivertMoZara", email = "worldmozara@163.com" },

scripts/wine_env.py

@@ -22,7 +22,7 @@ DEFAULT_WIN_PYTHON = "3.14"
 DEFAULT_WIN_UV_VERSION = "0.11.28"
 # typings/ is required for Wine basedpyright: pywinpty's shipped types are incomplete
 # (e.g. kill(sig) required); pyright default stubPath is ``typings/``.
-VIEW_LINKS = ("src", "tests", "scripts", "typings", "README.md", "LICENSE", "CLAUDE.md", "doc")
+VIEW_LINKS = ("src", "tests", "scripts", "typings", "README.md", "LICENSE", "AGENTS.md", "doc")
 VIEW_COPIES = ("pyproject.toml", "pdm.lock")
 
 

src/plyngent/agent/__init__.py

@@ -2,6 +2,7 @@ from .chat import ChatAgent as ChatAgent
 from .chat import get_lineno_read_files as get_lineno_read_files
 from .chat import invalidate_lineno_read as invalidate_lineno_read
 from .chat import lineno_read_lines as lineno_read_lines
+from .chat import lineno_read_mtime as lineno_read_mtime
 from .chat import mark_lineno_read as mark_lineno_read
 from .chat import reset_lineno_tracker as reset_lineno_tracker
 from .chat import was_lineno_read as was_lineno_read

src/plyngent/agent/chat.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from contextvars import ContextVar, Token
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 from msgspec import UNSET
@@ -47,14 +48,18 @@ if TYPE_CHECKING:
 
 
 # Per-conversation tracking of lines read with ``with_lineno=True``, keyed by
-# resolved file path. Set to a fresh ``dict`` at the start of each user turn via
-# :func:`reset_lineno_tracker`; cleared after the assistant finishes.
-# Tool handlers read/write via :func:`get_lineno_read_files` /
-# :func:`lineno_read_lines` / :func:`mark_lineno_read`.
-_lineno_read_files: ContextVar[dict[str, set[int]] | None] = ContextVar("_lineno_read_files", default=None)
+# resolved file path, with the file's mtime at read time (so stale line numbers
+# after external/process mutations are detected). Set to a fresh ``dict`` at the
+# start of each user turn via :func:`reset_lineno_tracker`; cleared after the
+# assistant finishes. Tool handlers read/write via :func:`get_lineno_read_files` /
+# :func:`lineno_read_lines` / :func:`lineno_read_mtime` / :func:`mark_lineno_read`.
+_lineno_read_files: ContextVar[dict[str, tuple[set[int], int]] | None] = ContextVar(
+    "_lineno_read_files",
+    default=None,
+)
 
 
-def reset_lineno_tracker() -> Token[dict[str, set[int]] | None]:
+def reset_lineno_tracker() -> Token[dict[str, tuple[set[int], int]] | None]:
     """Replace the tracker with a fresh empty mapping; return the previous token.
 
     Call at the start of a new user turn. Restore with
@@ -80,17 +85,38 @@ def lineno_read_lines(path: str) -> set[int]:
     val = _lineno_read_files.get()
     if val is None:
         return set()
-    return set(val.get(path, ()))
+    entry = val.get(path)
+    return set(entry[0]) if entry is not None else set()
+
+
+def lineno_read_mtime(path: str) -> int | None:
+    """Return the file mtime (ns) recorded when *path* was read, or None."""
+    val = _lineno_read_files.get()
+    if val is None:
+        return None
+    entry = val.get(path)
+    return entry[1] if entry is not None else None
 
 
 def mark_lineno_read(path: str, lines: set[int]) -> None:
     """Record that *path* was read with line numbers this turn.
 
     ``lines`` are 1-based absolute file line numbers (``read_file`` slice).
+    The file's current mtime is recorded too, so edits can detect that the
+    file changed since the read (external/process mutations included).
     """
     val = _lineno_read_files.get()
-    if val is not None:
-        val.setdefault(path, set()).update(lines)
+    if val is None:
+        return
+    try:
+        mtime_ns = Path(path).stat().st_mtime_ns
+    except OSError:
+        mtime_ns = 0
+    entry = val.get(path)
+    if entry is None:
+        val[path] = (set(lines), mtime_ns)
+    else:
+        val[path] = (entry[0] | lines, mtime_ns)
 
 
 def invalidate_lineno_read(path: str) -> None:
@@ -569,7 +595,8 @@ class ChatAgent:
         - Tools default **off**. ``tools=True`` clones this agent's registry with
           a **fresh session** bag (unless *session_state* is passed) and the
           given *instance_state* (CLI typically shares the host instance for
-          workspace identity).
+          workspace identity). A caller-built :class:`ToolRegistry` (e.g. a
+          ``clone(read_only_only=True)`` subset) is used as-is.
         """
         text = user_text.strip()
         if not text:

src/plyngent/agent/tools.py

@@ -42,6 +42,7 @@ class ToolTag(Flag):
     YOLO = auto()  # soft-confirm: eligible for YOLO auto-approve
     INSTANCE_STATE = auto()  # needs instance-scoped state
     SESSION_STATE = auto()  # needs session-scoped state
+    READ_ONLY = auto()  # never mutates host state; safe for read-only contexts
 
 
 class ToolDefinition:
@@ -266,14 +267,22 @@ class ToolRegistry:
         session_state: object | None = None,
         yolo: bool | None = None,
         auto_bind_state: bool | None = None,
+        read_only_only: bool = False,
     ) -> ToolRegistry:
         """New registry with the same tools/hooks and rebound host state.
 
         *instance_state* / *session_state* are applied as given (use the parent
         registry's handles only when the caller passes them through).
+
+        With *read_only_only*, only :attr:`ToolTag.READ_ONLY` tools are kept
+        (e.g. for safe side turns / planning); hooks and policy flags are
+        preserved.
         """
+        definitions = self.definitions()
+        if read_only_only:
+            definitions = [d for d in definitions if d.tags & ToolTag.READ_ONLY]
         return ToolRegistry(
-            self.definitions(),
+            definitions,
             danger=self._danger,
             on_confirm=self._on_confirm,
             yolo=self._yolo if yolo is None else yolo,

src/plyngent/cli/app.py

@@ -26,7 +26,7 @@ from plyngent.cli.state import ReplState
 from plyngent.config.models import DatabaseConfig
 from plyngent.memory import MemoryStore
 from plyngent.prompting import NonInteractiveBackend, configure_prompting
-from plyngent.runtime import ProviderNotSupportedError, create_client
+from plyngent.runtime import McpManager, ProviderNotSupportedError, create_client
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -124,9 +124,14 @@ def _read_prompt_text(prompt: str | None, *, stdin_isatty: bool) -> str | None:
     return text or None
 
 
-def _setup_hooks(*, interactive: bool) -> None:
-    """Install interactive limit hooks (workspace policy is set on ReplState)."""
-    if interactive:
+def _setup_hooks(*, interactive: bool, auto_continue: bool) -> None:
+    """Install limit hooks (workspace policy is set on ReplState).
+
+    ``auto_continue`` keeps the PTY/limit hook installed for one-shot runs so
+    ``--auto-continue`` / ``[agent] auto_continue_limits`` can raise limits
+    without a prompt; otherwise non-interactive runs keep today's deny.
+    """
+    if interactive or auto_continue:
         install_cli_limit_hooks()
     else:
         from plyngent.tools.process.pty_session import PtyManager
@@ -134,6 +139,24 @@ def _setup_hooks(*, interactive: bool) -> None:
         PtyManager.set_limit_continue_hook(None)
 
 
+async def _start_mcp_manager(store: ConfigStore) -> McpManager | None:
+    """Start configured MCP servers before the REPL state is built.
+
+    Returns ``None`` when nothing is enabled. Failures degrade to a warning
+    per server (the rest of the session, including LLM traffic, continues).
+    """
+    manager = McpManager(store.mcp_config)
+    if not manager.enabled_servers():
+        return None
+    await manager.ensure_started()
+    for name, status, count in manager.statuses():
+        if status.startswith("error"):
+            click.secho(f"warning: mcp server {name!r} failed: {status}", fg="yellow", err=True)
+        else:
+            click.secho(f"mcp: {name} ({status}, tools={count})", fg="bright_black", err=True)
+    return manager
+
+
 async def _bind_session(
     state: ReplState,
     *,
@@ -203,6 +226,7 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
     prompt_text: str | None,
     stream: bool,
     yes: bool,
+    auto_continue: bool,
     quiet: bool,
 ) -> int:
     oneshot = prompt_text is not None
@@ -218,7 +242,8 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
         if store.recoverable_providers:
             _warn_recoverable_providers(store.recoverable_providers)
 
-    _setup_hooks(interactive=interactive)
+    auto_effective = auto_continue or store.agent_config.auto_continue_limits
+    _setup_hooks(interactive=interactive, auto_continue=auto_effective)
     # --yes forces sticky YOLO; else derive from config.confirm_destructive.
     from plyngent.cli.state import YoloMode
 
@@ -285,6 +310,7 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
         except ProviderNotSupportedError as exc:
             raise click.ClickException(str(exc)) from exc
 
+        mcp_manager = await _start_mcp_manager(store)
         state = ReplState(
             config=store,
             memory=memory,
@@ -296,7 +322,9 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
             max_rounds=max_rounds,
             stream_enabled=stream,
             interactive_limits=interactive,
+            auto_continue_limits=auto_effective,
             yolo=yolo,
+            mcp_manager=mcp_manager,
         )
         # Path denylist and policy confirm live on instance.workspace (no process bag).
         state.instance_state.workspace.path_denylist = tuple(store.agent_config.path_denylist or ())
@@ -313,6 +341,10 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
                 prompt_policy_fetch_confirm,
                 instance=state.instance_state,
             )
+        from plyngent.tools.access import set_directory_access_confirm_hook
+
+        # Installed for one-shot too: the hook itself honours --yes / non-TTY.
+        set_directory_access_confirm_hook(state.directory_access_confirm_hook, instance=state.instance_state)
         # Seed cache if we already fetched; else warm in background for Tab.
         if remote_ids is not None:
             state.seed_remote_models(remote_ids)
@@ -353,6 +385,15 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
             set_fetch_policy_confirm_hook(None, instance=state_obj.instance_state)
             clear_private_grants(instance=state_obj.instance_state)
             clear_ssrf_assume_public_cidrs()
+            from plyngent.tools.access import clear_process_access, set_directory_access_confirm_hook
+
+            set_directory_access_confirm_hook(None, instance=state_obj.instance_state)
+            clear_process_access(instance=state_obj.instance_state)
+            from plyngent.cli.limits import reset_auto_continue
+
+            reset_auto_continue()
+            if state_obj.mcp_manager is not None:
+                await state_obj.mcp_manager.aclose()
             await state_obj.instance_state.shutdown()
         else:
             # No ReplState: only PTY class cleanup (temps require instance allowlist).
@@ -447,6 +488,12 @@ def main(ctx: click.Context, log_level: str) -> None:
     default=False,
     help="Enable YOLO: skip destructive-tool confirms (sticky for this process).",
 )
+@click.option(
+    "--auto-continue",
+    is_flag=True,
+    default=False,
+    help="Auto-raise tool/PTY limits without prompting (like answering yyy).",
+)
 @click.option(
     "--quiet",
     is_flag=True,
@@ -465,6 +512,7 @@ def chat_cmd(
     prompt: str | None,
     stream: bool,  # noqa: FBT001
     yes: bool,  # noqa: FBT001
+    auto_continue: bool,  # noqa: FBT001
     quiet: bool,  # noqa: FBT001
 ) -> None:
     """Interactive chat REPL, or one-shot with ``-p`` / stdin.
@@ -505,6 +553,7 @@ def chat_cmd(
             prompt_text=prompt_text,
             stream=stream,
             yes=yes,
+            auto_continue=auto_continue,
             quiet=quiet,
         )
     )

src/plyngent/cli/display.py

@@ -3,6 +3,8 @@ from __future__ import annotations
 import contextlib
 import json
 import os
+import re
+import shlex
 import sys
 from contextvars import ContextVar
 from typing import TYPE_CHECKING, Literal, cast
@@ -22,7 +24,7 @@ from plyngent.agent import (
 from plyngent.lmproto.openai_compatible.model import AssistantFunctionToolCall
 
 if TYPE_CHECKING:
-    from collections.abc import AsyncIterator
+    from collections.abc import AsyncIterator, Callable
 
     from plyngent.agent import AgentEvent
 
@@ -31,7 +33,29 @@ _TOOL_ARGS_PREVIEW = 80
 
 # Tool calls that render as a single pretty summary line instead of
 # ``[tool]`` / ``[tool result]``.
-_PRETTY_TOOLS = frozenset({"read_file", "todo_push", "todo_update"})
+_PRETTY_TOOLS = frozenset(
+    {
+        "read_file",
+        "todo_push",
+        "todo_update",
+        "tree",
+        "listdir",
+        "glob_paths",
+        "grep_files",
+        "run_argv",
+        "run_argv_batch",
+        "fetch",
+        "edit_replace",
+        "edit_lineno",
+        "write_file",
+        "copy_path",
+        "move_path",
+        "delete_path",
+        "vcs_status",
+        "vcs_log",
+        "wait",
+    }
+)
 
 # Process/session display flags (set from ReplState / slash).
 _verbose_tool_results: ContextVar[bool] = ContextVar("verbose_tool_results", default=False)
@@ -74,47 +98,330 @@ def _preview(text: str, limit: int) -> str:
     return text[:limit] + "…"
 
 
-def _json_str_arg(args_json: str, key: str) -> str | None:
-    """Extract a string argument from a tool-call arguments JSON blob."""
+def _preview_result(content: str, limit: int) -> str:
+    """Non-verbose tool-result preview: first line + a ``(…N more lines)`` tail."""
+    lines = content.splitlines()
+    if not lines:
+        return "(no output)"
+    first = _preview(lines[0], limit)
+    more = len(lines) - 1
+    if more == 0:
+        return first
+    unit = "line" if more == 1 else "lines"
+    return f"{first} (…{more} more {unit})"
+
+
+def _json_arg(args_json: str, key: str) -> object | None:
+    """Extract a single argument value (any type) from a tool-call args JSON blob."""
     try:
         raw = json.loads(args_json)
     except ValueError:
         return None
     if isinstance(raw, dict):
-        value = cast("dict[str, object]", raw).get(key)
-        if isinstance(value, str):
-            return value
+        return cast("dict[str, object]", raw).get(key)
     return None
 
 
+def _json_str_arg(args_json: str, key: str) -> str | None:
+    value = _json_arg(args_json, key)
+    return value if isinstance(value, str) else None
+
+
+def _json_list_arg(args_json: str, key: str) -> list[str] | None:
+    value = _json_arg(args_json, key)
+    if isinstance(value, list):
+        raw_items = cast("list[object]", value)
+        items = [item for item in raw_items if isinstance(item, str)]
+        if len(items) == len(raw_items):
+            return items
+    return None
+
+
+def _pretty_line(prefix: str, *segments: tuple[str, str | None]) -> str:
+    """Style a pretty tool summary: yellow ``* Verb`` prefix + colored detail segments.
+
+    ``segments`` are ``(text, fg)`` pairs; ``fg=None`` leaves a segment uncolored
+    and ``"dim"`` renders it dim. click.style emits ANSI codes only on a TTY,
+    so non-TTY output stays plain.
+    """
+    parts = [click.style(prefix, fg="yellow")]
+    for text, fg in segments:
+        if fg == "dim":
+            parts.append(click.style(text, dim=True))
+        else:
+            parts.append(click.style(text, fg=fg))
+    return "".join(parts)
+
+
 def _read_file_pretty(args_json: str, result: str) -> str:
     """One-line summary for a ``read_file`` call: ``* Read 'path' L1-4 (done)``."""
     path = _json_str_arg(args_json, "path") or "?"
     if result.startswith("error: file not found"):
-        return f"* Read '{path}' (file not found)"
+        return _pretty_line(f"* Read '{path}' ", ("(file not found)", "red"))
     if result.startswith("error: not a file"):
-        return f"* Read '{path}' (not a file)"
+        return _pretty_line(f"* Read '{path}' ", ("(not a file)", "red"))
     if result.startswith("error:"):
-        return f"* Read '{path}' (error)"
+        return _pretty_line(f"* Read '{path}' ", ("(error)", "red"))
     first = result.splitlines()[0] if result.splitlines() else ""
     if first.startswith("L") and "-" in first:
-        return f"* Read '{path}' {first} (done)"
-    return f"* Read '{path}' (done)"
+        return _pretty_line(f"* Read '{path}' ", (f"{first} ", "dim"), ("(done)", "green"))
+    return _pretty_line(f"* Read '{path}' ", ("(done)", "green"))
 
 
 def _todo_pretty(name: str, result: str) -> str:
     """Summary for todo push/update: header + the rendered todo stack."""
     label = "Todo Push" if name == "todo_push" else "Todo Update"
-    return f"* {label}:\n{result}"
+    return _pretty_line(f"* {label}:\n{result}")
+
+
+def _tree_line_stats(fmt: str, line: str) -> tuple[str, int] | None:
+    """Classify one ``tree`` result line as ``(kind, depth)`` or None (not an entry).
+
+    ``kind`` is ``"dir"`` or ``"file"``; depth is 0 for ``flat`` (no hierarchy).
+    """
+    stripped = line.strip()
+    if not stripped:
+        return None
+    kind: str | None = None
+    depth = 0
+    if fmt == "flat":
+        if not stripped.startswith("…"):
+            kind = "dir" if stripped.endswith("/") else "file"
+    elif fmt == "markdown":
+        if stripped.startswith("- ") and not stripped.startswith(("- …", "- error")):
+            kind = "dir" if stripped[2:].endswith("/") else "file"
+            depth = (len(line) - len(line.lstrip(" "))) // 2 + 1
+    elif "… (" not in stripped:
+        branch = "├── " if "├── " in line else ("└── " if "└── " in line else None)
+        if branch is not None:
+            name = line[line.index(branch) + len(branch) :].rstrip()
+            kind = "dir" if name.endswith("/") else "file"
+            depth = line.index(branch) // 4 + 1
+    if kind is None:
+        return None
+    return kind, depth
+
+
+def _tree_pretty(args_json: str, result: str) -> str:
+    """One-line summary for a ``tree`` call: ``* Tree 'src' (3 dirs, 24 files, depth 3)``.
+
+    Flat trees have no depth, so the depth part is omitted for ``format=flat``.
+    """
+    path = _json_str_arg(args_json, "path") or "."
+    fmt = _json_str_arg(args_json, "format") or "markdown"
+    if result.startswith("error:"):
+        return f"* Tree '{path}' (error)"
+    dirs = 0
+    files = 0
+    depth = 0
+    for line in result.splitlines():
+        stats = _tree_line_stats(fmt, line)
+        if stats is None:
+            continue
+        kind, line_depth = stats
+        if kind == "dir":
+            dirs += 1
+        else:
+            files += 1
+        depth = max(depth, line_depth)
+    if depth:
+        return _pretty_line(f"* Tree '{path}' ", (f"({dirs} dirs, {files} files, depth {depth})", None))
+    return _pretty_line(f"* Tree '{path}' ", (f"({dirs} dirs, {files} files)", None))
+
+
+def _listdir_pretty(args_json: str, result: str) -> str:
+    """One-line summary for a ``listdir`` call: ``* List 'path' (3 dirs, 5 files)``."""
+    path = _json_str_arg(args_json, "path") or "."
+    if result.startswith("error:"):
+        return _pretty_line(f"* List '{path}' ", (f"({result})", "red"))
+    if result == "(empty)":
+        return _pretty_line(f"* List '{path}' ", ("(empty)", "dim"))
+    dirs = 0
+    files = 0
+    for line in result.splitlines():
+        if line.startswith("dir\t"):
+            dirs += 1
+        elif line.startswith("file\t"):
+            files += 1
+    return _pretty_line(f"* List '{path}' ", (f"({dirs} dirs, {files} files)", None))
+
+
+def _glob_pretty(args_json: str, result: str) -> str:
+    """One-line summary for a ``glob_paths`` call: ``* Glob '**/*.py' in '.' (12 paths)``."""
+    pattern = _json_str_arg(args_json, "pattern") or "?"
+    path = _json_str_arg(args_json, "path") or "."
+    if result.startswith("error:"):
+        return _pretty_line(f"* Glob '{pattern}' in '{path}' ", (f"({result})", "red"))
+    if result == "(no matches)":
+        return _pretty_line(f"* Glob '{pattern}' in '{path}' ", ("(no matches)", "dim"))
+    count = sum(1 for line in result.splitlines() if line and not line.startswith("...[truncated"))
+    unit = "path" if count == 1 else "paths"
+    return _pretty_line(f"* Glob '{pattern}' in '{path}' ", (f"({count} {unit})", None))
+
+
+def _grep_pretty(args_json: str, result: str) -> str:
+    """One-line summary for a ``grep_files`` call: ``* Grep 'pat' in '.' (12 matches in 3 files)``."""
+    pattern = _json_str_arg(args_json, "pattern") or "?"
+    path = _json_str_arg(args_json, "path") or "."
+    if result.startswith("error:"):
+        return _pretty_line(f"* Grep '{pattern}' in '{path}' ", (f"({result})", "red"))
+    if result == "(no matches)":
+        return _pretty_line(f"* Grep '{pattern}' in '{path}' ", ("(no matches)", "dim"))
+    matches = [line for line in result.splitlines() if line and not line.startswith("...[truncated")]
+    files = len({line.split(":", 1)[0] for line in matches})
+    match_unit = "match" if len(matches) == 1 else "matches"
+    file_unit = "file" if files == 1 else "files"
+    return _pretty_line(
+        f"* Grep '{pattern}' in '{path}' ",
+        (f"({len(matches)} {match_unit} in {files} {file_unit})", None),
+    )
+
+
+def _run_argv_pretty(args_json: str, result: str) -> str:
+    """One-line summary for a ``run_argv`` call: ``* Run $ git status --short (exit code 0)``."""
+    argv = _json_list_arg(args_json, "argv")
+    cmd = shlex.join(argv) if argv else "?"
+    if result.startswith("error:"):
+        return _pretty_line(f"* Run $ {cmd} ", (f"({result})", "red"))
+    fields: dict[str, str] = {}
+    for line in result.splitlines():
+        if line.startswith("--- "):
+            break
+        if "=" in line:
+            key, _, value = line.partition("=")
+            fields[key] = value
+    if fields.get("timed_out") == "true":
+        return _pretty_line(f"* Run $ {cmd} ", ("(timed out)", "red"))
+    code = fields.get("exit_code", "")
+    fg = "green" if code == "0" else "red"
+    return _pretty_line(f"* Run $ {cmd} ", (f"(exit code {code or 'killed'})", fg))
+
+
+def _run_argv_batch_pretty(_args_json: str, result: str) -> str:
+    """One-line summary for a ``run_argv_batch`` call: ``* Run batch (done)``."""
+    if result.startswith("error:"):
+        return _pretty_line("* Run batch ", (f"({result})", "red"))
+    lines = result.splitlines()
+    head = lines[0] if lines else ""
+    stopped_early = False
+    for part in head.split():
+        if part == "stopped_early=true":
+            stopped_early = True
+    if stopped_early:
+        return _pretty_line("* Run batch ", ("(stopped early)", "yellow"))
+    return _pretty_line("* Run batch ", ("(done)", "green"))
+
+
+def _http_status_fg(status: str) -> str | None:
+    """Foreground color by HTTP status class (2xx green, 3xx yellow, 4xx/5xx red)."""
+    if status and status[0] in {"2", "3", "4", "5"}:
+        return {"2": "green", "3": "yellow", "4": "red", "5": "red"}[status[0]]
+    return None
+
+
+def _fetch_pretty(args_json: str, result: str) -> str:
+    """One-line summary for a ``fetch`` call: ``* Fetch GET https://… (200)``."""
+    method = _json_str_arg(args_json, "method") or "GET"
+    url = _json_str_arg(args_json, "url") or "?"
+    if result.startswith("error:"):
+        return _pretty_line(f"* Fetch {method} {url} ", (f"({result})", "red"))
+    status = ""
+    for line in result.splitlines():
+        if line.startswith("--- "):
+            break
+        if line.startswith("status="):
+            status = line.partition("=")[2]
+            break
+    return _pretty_line(f"* Fetch {method} {url} ", (f"({status or 'done'})", _http_status_fg(status)))
+
+
+_MUTATOR_VERBS: dict[str, str] = {
+    "edit_replace": "Edit",
+    "edit_lineno": "Edit",
+    "write_file": "Write",
+    "copy_path": "Copy",
+    "move_path": "Move",
+    "delete_path": "Delete",
+}
+
+
+def _mutator_pretty(name: str, args_json: str, result: str) -> str:
+    """One-line summary for a file mutation: ``* Wrote 'path' (120 chars)`` / ``* Edit 'path' (done)``."""
+    verb = _MUTATOR_VERBS[name]
+    if name in {"copy_path", "move_path"}:
+        src = _json_str_arg(args_json, "src") or "?"
+        dst = _json_str_arg(args_json, "dst") or "?"
+        target = f"'{src}' → '{dst}'"
+    else:
+        path = _json_str_arg(args_json, "path") or "?"
+        target = f"'{path}'"
+    if result.startswith("error:"):
+        return _pretty_line(f"* {verb} {target} ", (f"({result})", "red"))
+    if name == "write_file":
+        # write_file keeps its brief detail: ``wrote 120 characters to path``.
+        match = re.match(r"wrote (\d+) characters to (.+)$", result)
+        if match:
+            chars, path = match.groups()
+            return _pretty_line(f"* Write '{path}' ", (f"({chars} chars)", None))
+    return _pretty_line(f"* {verb} {target} ", ("(done)", "green"))
+
+
+def _vcs_status_pretty(_args_json: str, result: str) -> str:
+    """One-line summary for ``vcs_status``: ``* VCS Status (done)``."""
+    if result.startswith("error:"):
+        return _pretty_line("* VCS Status ", (f"({result})", "red"))
+    return _pretty_line("* VCS Status ", ("(done)", "green"))
+
+
+def _vcs_log_pretty(_args_json: str, result: str) -> str:
+    """One-line summary for ``vcs_log``: ``* VCS Log (5 commits)``."""
+    if result.startswith("error:"):
+        return _pretty_line("* VCS Log ", (f"({result})", "red"))
+    if result == "(no commits)":
+        return _pretty_line("* VCS Log ", ("(no commits)", "dim"))
+    commits = [line for line in result.splitlines() if line.strip()]
+    unit = "commit" if len(commits) == 1 else "commits"
+    return _pretty_line("* VCS Log ", (f"({len(commits)} {unit})", None))
+
+
+def _wait_pretty(_args_json: str, result: str) -> str:
+    """One-line summary for a ``wait`` call: ``* Wait (5s)`` / ``* Wait (disturbed)``."""
+    if result.startswith("error:"):
+        return _pretty_line("* Wait ", (f"({result})", "red"))
+    if result.startswith("waited "):
+        return _pretty_line("* Wait ", (f"({result.removeprefix('waited ')})", "green"))
+    return _pretty_line("* Wait ", ("(disturbed)", "yellow"))
+
+
+_PRETTY_BUILDERS: dict[str, Callable[[str, str], str]] = {
+    "read_file": _read_file_pretty,
+    "tree": _tree_pretty,
+    "todo_push": lambda _args, result: _todo_pretty("todo_push", result),
+    "todo_update": lambda _args, result: _todo_pretty("todo_update", result),
+    "listdir": _listdir_pretty,
+    "glob_paths": _glob_pretty,
+    "grep_files": _grep_pretty,
+    "run_argv": _run_argv_pretty,
+    "run_argv_batch": _run_argv_batch_pretty,
+    "fetch": _fetch_pretty,
+    "edit_replace": lambda args, result: _mutator_pretty("edit_replace", args, result),
+    "edit_lineno": lambda args, result: _mutator_pretty("edit_lineno", args, result),
+    "write_file": lambda args, result: _mutator_pretty("write_file", args, result),
+    "copy_path": lambda args, result: _mutator_pretty("copy_path", args, result),
+    "move_path": lambda args, result: _mutator_pretty("move_path", args, result),
+    "delete_path": lambda args, result: _mutator_pretty("delete_path", args, result),
+    "vcs_status": _vcs_status_pretty,
+    "vcs_log": _vcs_log_pretty,
+    "wait": _wait_pretty,
+}
 
 
 def _pretty_tool_result(name: str, args_json: str, result: str) -> str | None:
     """Pretty summary for a known tool call + result; None keeps the old style."""
-    if name == "read_file":
-        return _read_file_pretty(args_json, result)
-    if name in {"todo_push", "todo_update"}:
-        return _todo_pretty(name, result)
-    return None
+    builder = _PRETTY_BUILDERS.get(name)
+    if builder is None:
+        return None
+    return builder(args_json, result)
 
 
 def _echo_stream(text: str) -> None:
@@ -258,14 +565,13 @@ async def render_events(  # noqa: C901, PLR0912, PLR0915
             content = event.message.content
             name, args, pretty_tool = pending_tools.pop(0) if pending_tools else ("", "", False)
             pretty_line = _pretty_tool_result(name, args, content) if pretty_tool else None
-            if pretty_line is not None:
-                click.secho(f"\n{pretty_line}", fg="yellow")
+            if pretty_line is not None and not show_full:
+                click.echo(f"\n{pretty_line}")
             elif show_full:
                 click.secho(f"[tool ok]\n{content}", fg="magenta")
             else:
-                preview = _preview(content, _TOOL_RESULT_PREVIEW)
-                one_line = preview.replace("\n", " ")
-                click.secho(f"[tool ok] {one_line}", fg="magenta")
+                preview = _preview_result(content, _TOOL_RESULT_PREVIEW)
+                click.secho(f"[tool ok] {preview}", fg="magenta")
         elif isinstance(event, ErrorEvent):
             flush_assistant()
             suffix = ""

src/plyngent/cli/limits.py

@@ -4,6 +4,7 @@ import contextlib
 import selectors
 import shutil
 import sys
+from dataclasses import dataclass
 from typing import TYPE_CHECKING, Literal
 
 from plyngent.cli.interrupt import pause_task_cancel_for_prompt
@@ -18,16 +19,56 @@ from plyngent.prompting import (
     confirm,
     get_prompt_backend,
 )
+from plyngent.tools.access import AccessDecision
 from plyngent.tools.process.pty_session import PtyManager
+from plyngent.tools.workspace import AccessMode, parse_access_mode
 
 if TYPE_CHECKING:
     from collections.abc import Mapping, Sequence
+    from pathlib import Path
 type WorkspaceMismatchChoice = Literal["keep", "rebind", "abort"]
 
 _BOX_MIN_WIDTH = 40
 _BOX_MAX_WIDTH = 100
 _BOX_PAD = 2  # spaces inside left/right borders
 
+# Limit prompts accept ``yyy`` to stop asking for the rest of the turn.
+_CONTINUE_PROMPT = "Raise limit and continue? [Y/n/yyy] (yyy = stop asking this turn): "
+_CONTINUE_YES_TOKENS = frozenset({"", "y", "yes"})
+_CONTINUE_AUTO_TOKEN = "yyy"
+
+
+@dataclass
+class _AutoContinue:
+    """Auto-continue layers: process default (flag/config) + ``yyy`` turn skip."""
+
+    default: bool = False
+    turn: bool = False
+
+
+_auto_continue = _AutoContinue()
+
+
+def auto_continue_enabled() -> bool:
+    """Whether limit prompts are auto-approved (process default or ``yyy``)."""
+    return _auto_continue.default or _auto_continue.turn
+
+
+def set_auto_continue_default(*, enabled: bool) -> None:
+    """Set the process-wide default (``--auto-continue`` / ``[agent]`` config)."""
+    _auto_continue.default = bool(enabled)
+
+
+def reset_auto_continue_turn() -> None:
+    """Clear the ``yyy`` skip at a turn boundary."""
+    _auto_continue.turn = False
+
+
+def reset_auto_continue() -> None:
+    """Clear both layers (chat exit / tests)."""
+    _auto_continue.default = False
+    _auto_continue.turn = False
+
 
 def _terminal_width() -> int:
     try:
@@ -104,10 +145,33 @@ def _echo_continue_limit(reason: str) -> None:
     backend.echo()
 
 
+def _echo_auto_continue(reason: str) -> None:
+    """Echo the limit reason plus the ``yyy`` notice (no prompt)."""
+    backend = get_prompt_backend()
+    backend.secho(f"[limit] {reason}", fg="yellow")
+    backend.secho("[limit] auto-continuing (yyy) — no more limit prompts this turn", fg="bright_black")
+    backend.echo()
+
+
+def _decide_continue_limit(reason: str) -> bool:
+    """Shared limit decision for the sync/async prompts (may read a line)."""
+    if auto_continue_enabled():
+        _echo_auto_continue(reason)
+        return True
+    backend = get_prompt_backend()
+    if not backend.is_interactive():
+        return False
+    _echo_continue_limit(reason)
+    token = backend.read_line(_CONTINUE_PROMPT, default="y").strip().lower()
+    if token == _CONTINUE_AUTO_TOKEN:
+        _auto_continue.turn = True
+        return True
+    return token in _CONTINUE_YES_TOKENS
+
+
 def _prompt_continue_limit_sync(reason: str) -> bool:
     try:
-        _echo_continue_limit(reason)
-        return confirm("Raise limit and continue?", default=True)
+        return _decide_continue_limit(reason)
     except NonInteractiveError:
         return False
 
@@ -119,15 +183,11 @@ def prompt_continue_limit(reason: str) -> bool:
 
 
 async def prompt_continue_limit_async(reason: str) -> bool:
-    """Async variant: confirm off the event loop so the turn is not cancelled."""
+    """Async variant: prompt off the event loop so the turn is not cancelled."""
     try:
         from plyngent.prompting import run_prompt_async
 
-        def _run() -> bool:
-            _echo_continue_limit(reason)
-            return confirm("Raise limit and continue?", default=True)
-
-        return await run_prompt_async(_run)
+        return await run_prompt_async(lambda: _decide_continue_limit(reason))
     except NonInteractiveError:
         return False
 
@@ -287,6 +347,62 @@ def prompt_policy_fetch_confirm(
         return False
 
 
+def prompt_directory_access_confirm(
+    path: Path,
+    mode: AccessMode,
+    reason: str,
+    timeout_seconds: float,
+) -> AccessDecision | str | None:
+    """Ask whether to grant access to *path* at *mode* (timed; default deny).
+
+    ``y`` approves the requested level; ``read`` / ``write`` / ``exec`` approve
+    that level instead. The host's hook decides YOLO/``--yes`` before calling
+    this. Timeout, cancel, or non-interactive → ``None`` (deny).
+    """
+    lines = [
+        f"request: {mode.name.lower()} access to {path}",
+        f"kind: {'directory' if path.is_dir() else 'file'}",
+    ]
+    if reason:
+        lines.append(f"why: {reason}")
+    lines.append(f"(timeout {timeout_seconds:g}s defaults to DENY)")
+    try:
+        with pause_task_cancel_for_prompt():
+            backend = get_prompt_backend()
+            if not backend.is_interactive():
+                return None
+            backend.echo()
+            backend.secho(
+                format_tool_confirm_box("request_directory_access", "\n".join(lines)),
+                fg="yellow",
+            )
+            backend.echo()
+            prompt = (
+                f"[access] allow {path} ({mode.name.lower()})? [y/N|read|write|exec] (timeout {timeout_seconds:g}s): "
+            )
+            with contextlib.suppress(OSError):
+                _ = sys.stderr.write(prompt)
+                _ = sys.stderr.flush()
+            raw = _read_yes_no_line_with_timeout(timeout_seconds)
+            if raw is None:
+                with contextlib.suppress(OSError, NonInteractiveError):
+                    backend.secho(
+                        f"[access] timed out after {timeout_seconds:g}s — denied",
+                        fg="red",
+                        err=True,
+                    )
+                return None
+            token = raw.strip().lower()
+            if token in {"y", "yes"}:
+                return AccessDecision(mode)
+            level = parse_access_mode(token)
+            if level is not None:
+                return AccessDecision(level)
+            return None
+    except NonInteractiveError, KeyboardInterrupt, EOFError:
+        return None
+
+
 async def prompt_confirm_tool_async(name: str, args: Mapping[str, object], reason: str) -> bool | str:
     """Async confirm: True allow, False deny, str = deny with user comment."""
     del args

src/plyngent/cli/repl.py

@@ -36,14 +36,17 @@ def _echo_interrupted() -> None:
 async def run_repl(state: ReplState) -> None:
     """Interactive chat loop with readline editing, history, and Tab completion."""
     setup_readline(state)
+    from plyngent.cli.limits import auto_continue_enabled
+
     yolo = state.effective_yolo()
     yolo_part = f"  yolo={yolo}" if yolo != "off" else ""
+    auto_part = "  limit_auto=on" if auto_continue_enabled() else ""
     click.echo(
         f"plyngent chat  provider={state.provider_name}  model={state.model}  "
         f"session={state.session_id}  tools={'on' if state.tools_enabled else 'off'}  "
         f"rounds={state.max_rounds}  messages={len(state.agent.messages)}  "
         f"stream={'on' if state.agent.stream else 'off'}  "
-        f"verbose={'on' if state.verbose else 'off'}{yolo_part}"
+        f"verbose={'on' if state.verbose else 'off'}{yolo_part}{auto_part}"
     )
     click.echo('Type /help for commands. Multiline: """ … """. Empty line is ignored.')
 

src/plyngent/cli/retry.py

@@ -10,6 +10,7 @@ import click
 
 from plyngent.cli.display import render_events
 from plyngent.cli.interrupt import allow_task_cancel, set_sigint_reinstall
+from plyngent.cli.limits import reset_auto_continue_turn
 
 if TYPE_CHECKING:
     from collections.abc import AsyncIterator, Callable, Coroutine
@@ -184,7 +185,23 @@ async def run_turn_with_retries(
     further attempts use ``agent.retry`` so the user message is not duplicated.
 
     Ctrl+C cancels the in-flight task; user message stays in DB for ``/retry``.
+
+    The ``yyy`` limit auto-continue is turn-scoped: cleared before and after the
+    turn, so a retry of the same turn keeps it but the next user turn prompts.
     """
+    reset_auto_continue_turn()
+    try:
+        return await _run_turn_with_retries(agent, starter=starter, delays=delays)
+    finally:
+        reset_auto_continue_turn()
+
+
+async def _run_turn_with_retries(
+    agent: ChatAgent,
+    *,
+    starter: Callable[[], AsyncIterator[AgentEvent]],
+    delays: tuple[float, ...],
+) -> bool:
     max_retries = len(delays)
     attempt = 0
     current: Callable[[], AsyncIterator[AgentEvent]] = starter

src/plyngent/cli/slash.py

@@ -24,6 +24,7 @@ from plyngent.runtime import ProviderNotSupportedError
 if TYPE_CHECKING:
     from collections.abc import Awaitable, Sequence
 
+    from plyngent.agent import ToolRegistry
     from plyngent.cli.state import ReplState, YoloMode
     from plyngent.lmproto.openai_compatible.model import AnyChatMessage
 
@@ -83,7 +84,8 @@ HELP_FOOTER = (
     "works after resume, not only via readline history). Auto-retry: 10s/20s/30s.\n"
     "\n"
     "Side questions: /btw … answers without changing the main session\n"
-    "(optional --tools / --fresh). Tab completes slash commands and arguments.\n"
+    "(--tools=read by default: read-only tools; --tools no/full opt-in; --fresh).\n"
+    "Tab completes slash commands and arguments.\n"
     "Use --session ID or /resume to continue a prior chat after restart.\n"
     "\n"
     'Multiline: start a message with """ then end a later line with """.\n'
@@ -519,6 +521,7 @@ def config_cmd(state: ReplState) -> None:
 def status_cmd(state: ReplState) -> None:
     """Show session/provider/tools/rounds status."""
     from plyngent.agent.budget import estimate_messages_chars
+    from plyngent.tools.access import access_grant_rows
 
     pending = state.agent.pending_retry_text
     pending_disp = "yes" if pending else "no"
@@ -553,6 +556,7 @@ def status_cmd(state: ReplState) -> None:
         f"usage_last_turn={last_u.format_line(billed=True)}  "
         f"rounds={last_rounds}\n"
         f"usage_session={session_u.format_line(billed=True)}\n"
+        f"grants={len(access_grant_rows(instance=state.instance_state, session=state.session_state))}  "
         f"workspace={state.workspace}"
     )
 
@@ -928,11 +932,12 @@ def _format_tool_tags(tags: object) -> str:
 @slash.command("btw")
 @click.argument("question", nargs=-1, required=False)
 @click.option(
-    "--tools/--no-tools",
-    "with_tools",
-    default=False,
+    "--tools",
+    "tools_mode",
+    type=click.Choice(["no", "read", "full"]),
+    default="read",
     show_default=True,
-    help="Allow tools on the side turn (shared workspace; forked session grants/todo).",
+    help=("Tool access on the side turn: read = read-only tools only (default), no = no tools, full = all tools."),
 )
 @click.option(
     "--fresh",
@@ -945,54 +950,85 @@ def btw_cmd(
     state: ReplState,
     question: tuple[str, ...],
     *,
-    with_tools: bool,
+    tools_mode: str,
     fresh: bool,
 ) -> None:
     """Ask a side question without changing the main session transcript or DB.
 
     Uses the current model and (unless ``--fresh``) a copy of main history.
-    Tools are **off** by default; ``--tools`` clones the main tool registry with
-    a fresh session bag and the shared instance workspace.
+    Tools default to **read-only** (``--tools=read``): file/vcs/ask/fetch-GET
+    reads with no state mutation. ``--tools=no`` turns tools off and
+    ``--tools=full`` clones the whole main registry with a fresh session bag
+    and the shared instance workspace.
     """
     text = " ".join(question).strip()
     if not text:
-        click.echo("usage: /btw [--tools] [--fresh] <question>")
+        click.echo("usage: /btw [--tools read|no|full] [--fresh] <question>")
         return
     if state.agent.pending_retry_text is not None:
         click.echo("error: finish or /retry the main turn before /btw")
         return
-    if with_tools and (not state.tools_enabled or state.agent.tools is None):
-        click.echo("error: --tools requires tools on (/tools on)")
-        return
+
+    tools_on = state.tools_enabled and state.agent.tools is not None
+    explicit = click.get_current_context().get_parameter_source("tools_mode") is not click.core.ParameterSource.DEFAULT
+    if tools_mode != "no" and not tools_on:
+        # Explicitly requesting tools while they are off is an error; the
+        # default (read) silently falls back to no tools so bare /btw still
+        # works under /tools off.
+        if tools_mode == "full" or explicit:
+            click.echo("error: --tools requires tools on (/tools on)")
+            return
+        tools_mode = "no"
 
     from plyngent.cli.display import render_events
     from plyngent.cli.retry import run_cancellable
-    from plyngent.tools.context import SessionState
+    from plyngent.tools.context import SessionState, read_only_context
 
     click.secho("btw: ", fg="magenta", nl=False)
     click.echo(text)
-    tools_arg: bool = with_tools
-    aside_session = SessionState() if with_tools else None
-    aside_instance = state.instance_state if with_tools else None
+    if tools_mode == "no":
+        tools_arg: ToolRegistry | bool = False
+        aside_session = None
+        aside_instance = None
+    elif tools_mode == "full":
+        tools_arg = True
+        aside_session = SessionState()
+        aside_instance = state.instance_state
+    else:  # read
+        assert state.agent.tools is not None
+        # Read-only clone: keep the main session view so read-only session
+        # reads (e.g. todo_list) see the real state (they cannot mutate it).
+        tools_arg = state.agent.tools.clone(read_only_only=True)
+        aside_session = state.session_state
+        aside_instance = state.instance_state
 
     async def _run() -> None:
-        await run_cancellable(
-            render_events(
-                state.agent.run_aside(
-                    text,
-                    include_history=not fresh,
-                    tools=tools_arg,
-                    instance_state=aside_instance,
-                    session_state=aside_session,
-                )
+        side = render_events(
+            state.agent.run_aside(
+                text,
+                include_history=not fresh,
+                tools=tools_arg,
+                instance_state=aside_instance,
+                session_state=aside_session,
             )
         )
+        if tools_mode == "read":
+            with read_only_context():
+                await run_cancellable(side)
+        else:
+            await run_cancellable(side)
 
+    from plyngent.cli.limits import reset_auto_continue_turn
+
+    # Aside is its own exchange: a ``yyy`` from the main turn must not leak in.
+    reset_auto_continue_turn()
     try:
         _await(_run())
     except Exception as exc:  # noqa: BLE001 — surface side-turn failures
         click.secho(f"error: btw failed: {exc}", fg="red")
         return
+    finally:
+        reset_auto_continue_turn()
     click.secho("(btw done — main session unchanged)", fg="bright_black")
 
 
@@ -1119,6 +1155,128 @@ def plugins_slash_cmd(state: ReplState, action: str | None, name: str | None) ->
         raise click.UsageError(str(exc)) from exc
 
 
+_MCP_PREVIEW_MAX_CHARS = 120
+
+
+def _print_mcp_status(state: ReplState) -> None:
+    manager = state.mcp_manager
+    if manager is None:
+        click.echo("mcp: no servers configured (or none enabled)")
+        return
+    rows = manager.statuses()
+    if not rows:
+        click.echo("mcp: no servers configured (or none enabled)")
+        return
+    for name, status, count in rows:
+        click.echo(f"  {name}\t{status}\ttools={count}")
+        connection = next(
+            (conn for conn in manager.connections() if conn.name == name),
+            None,
+        )
+        if connection is not None and connection.instructions:
+            preview = " ".join(connection.instructions.split())
+            if len(preview) > _MCP_PREVIEW_MAX_CHARS:
+                preview = f"{preview[: _MCP_PREVIEW_MAX_CHARS - 3]}..."
+            click.secho(
+                f"    instructions ({len(connection.instructions)} chars): {preview}",
+                fg="bright_black",
+            )
+        if connection is not None and connection.error is not None:
+            for line in connection.stderr_tail()[-3:]:
+                click.secho(f"    {line}", fg="bright_black")
+
+
+@slash.command("mcp")
+@click.argument("action", required=False, type=click.Choice(["list", "reconnect"]))
+@click.pass_obj
+def mcp_slash_cmd(state: ReplState, action: str | None) -> None:
+    """List MCP server statuses, or reconnect after config edits.
+
+    ``/mcp`` or ``/mcp list`` — per-server connection status and tool count.
+    ``/mcp reconnect`` — re-read the config file, restart every enabled
+    server, and rebuild the tool registry (adopts newly added servers too).
+    """
+    act = (action or "list").lower()
+    if act == "list":
+        _print_mcp_status(state)
+        return
+    from plyngent.runtime import McpManager
+
+    state.config.reload()
+    if state.mcp_manager is None:
+        state.mcp_manager = McpManager(state.config.mcp_config)
+    else:
+        _await(state.mcp_manager.restart(state.config.mcp_config))
+    _await(state.mcp_manager.ensure_started())
+    _slash_rebuild_tools_if_on(state)
+    click.echo(f"mcp reconnected; tools={'on' if state.tools_enabled else 'off'}")
+    _print_mcp_status(state)
+
+
+@slash.command("grants")
+@click.argument("action", required=False, type=click.Choice(["list", "revoke"]))
+@click.argument("target", required=False)
+@click.pass_obj
+def grants_cmd(state: ReplState, action: str | None, target: str | None) -> None:
+    """List or revoke directory-access grants.
+
+    ``/grants`` or ``/grants list`` — session, process, then config grants.
+    ``/grants revoke <index|all>`` — drop one grant or all session/process
+    grants. Config grants come from ``[agent].allow_paths``; edit the TOML.
+    """
+    from plyngent.tools.access import (
+        access_grant_rows,
+        clear_process_access,
+        clear_session_access,
+        revoke_access,
+    )
+
+    act = (action or "list").lower()
+    if act == "list":
+        rows = access_grant_rows(instance=state.instance_state, session=state.session_state)
+        if not rows:
+            click.echo("no directory-access grants")
+            return
+        click.echo(f"directory-access grants ({len(rows)}):")
+        for index, (path, mode, source) in enumerate(rows):
+            click.echo(f"  {index}\t{path}\t{mode.name.lower()}\t{source}")
+        click.echo("revoke with /grants revoke <index> or /grants revoke all")
+        return
+
+    if target is None or not target.strip():
+        msg = "/grants revoke requires an index or 'all'"
+        raise click.UsageError(msg)
+    token = target.strip().lower()
+    if token == "all":
+        clear_session_access(session=state.session_state)
+        clear_process_access(instance=state.instance_state)
+        _await(state.persist_access_grants())
+        click.echo("revoked all session/process access grants (config grants unchanged)")
+        return
+    if not token.isdigit():
+        msg = "/grants revoke expects an index or 'all'"
+        raise click.UsageError(msg)
+    rows = access_grant_rows(instance=state.instance_state, session=state.session_state)
+    index = int(token)
+    if index < 0 or index >= len(rows):
+        msg = f"no grant at index {index}"
+        raise click.UsageError(msg)
+    path, _mode, source = rows[index]
+    if source == "config":
+        click.echo(f"config grant {path} is not revocable here; edit [agent].allow_paths")
+        return
+    if revoke_access(
+        path,
+        source=source,
+        instance=state.instance_state,
+        session=state.session_state,
+    ):
+        _await(state.persist_access_grants())
+        click.echo(f"revoked {path} ({source})")
+    else:
+        click.echo(f"grant not found: {path}")
+
+
 @slash.command("yolo")
 @click.argument("mode", required=False, type=YOLO_MODE, metavar="[on|off|once]")
 @click.pass_obj

src/plyngent/cli/state.py

@@ -26,16 +26,31 @@ from plyngent.tools import InstanceState, SessionState
 from plyngent.tools.view import MemoryViewStore, session_data_view
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Mapping, Sequence
 
     from plyngent.config.models import Provider
     from plyngent.config.store import ConfigStore
     from plyngent.memory import MemoryStore
     from plyngent.memory.database.schema import Session as SessionRow
+    from plyngent.runtime.mcp_client import McpManager
+    from plyngent.tools.access import AccessDecision
+    from plyngent.tools.workspace import AccessMode
 
 type YoloMode = Literal["off", "on", "once"]
 
 
+def _parsed_access_grants(raw: Mapping[str, str]) -> dict[Path, AccessMode]:
+    """Parse stored ``{path: mode}`` grants into resolved keys (skip bad modes)."""
+    from plyngent.tools.workspace import parse_access_mode
+
+    grants: dict[Path, AccessMode] = {}
+    for path_str, mode_str in raw.items():
+        mode = parse_access_mode(mode_str)
+        if mode is not None:
+            grants[Path(path_str).expanduser().resolve()] = mode
+    return grants
+
+
 @dataclass
 class ReplState:
     """Mutable REPL session state."""
@@ -54,6 +69,8 @@ class ReplState:
     markdown_enabled: bool = True
     # One-shot / scripts: never prompt to raise tool-loop limits.
     interactive_limits: bool = True
+    # Auto-raise tool/PTY limits without prompting (--auto-continue / config).
+    auto_continue_limits: bool = False
     # Soft destructive-tool confirms: None → derive from config.confirm_destructive.
     # off = confirm; on = skip (sticky); once = skip next user turn then off.
     yolo: YoloMode | None = None
@@ -65,6 +82,8 @@ class ReplState:
     todo_stack: TodoStack = field(default_factory=TodoStack)
     instance_state: InstanceState = field(default_factory=InstanceState)
     session_state: SessionState = field(default_factory=SessionState)
+    # MCP connections started by the host app before this state was built.
+    mcp_manager: McpManager | None = None
     _todo_persist_tasks: set[object] = field(default_factory=set, init=False, repr=False)
     # Session ids for Tab complete (updated when listing/creating/resuming).
     _session_id_cache: list[int] = field(default_factory=list, init=False, repr=False)
@@ -79,6 +98,10 @@ class ReplState:
         self.workspace = Path(self.workspace).expanduser().resolve()
         self.instance_state.workspace_root = self.workspace
         self.instance_state.workspace.root = self.workspace
+        self._install_config_access()
+        from plyngent.cli.limits import set_auto_continue_default
+
+        set_auto_continue_default(enabled=self.auto_continue_limits)
         self.session_state = self._session_data_for_todo()
         self.agent = self._make_agent()
         self.sync_display_flags()
@@ -90,6 +113,12 @@ class ReplState:
         set_verbose_tool_results(self.verbose)
         set_markdown_enabled(self.markdown_enabled)
 
+    def _reset_limit_auto_continue(self) -> None:
+        """Drop a ``yyy`` skip on session change (it is turn-scoped)."""
+        from plyngent.cli.limits import reset_auto_continue_turn
+
+        reset_auto_continue_turn()
+
     def _workspace_key(self) -> str:
         key = normalize_workspace(self.workspace)
         if key is None:
@@ -145,11 +174,17 @@ class ReplState:
         self._todo_persist_tasks.add(task)
         task.add_done_callback(self._todo_persist_tasks.discard)
 
-    def _session_data_for_todo(self, *, grants: dict[str, bool] | None = None) -> SessionState:
+    def _session_data_for_todo(
+        self,
+        *,
+        grants: dict[str, bool] | None = None,
+        access_grants: dict[Path, AccessMode] | None = None,
+    ) -> SessionState:
         """Build a SessionState with live todo + MemoryViewStore seed (durable tree).
 
         *grants* defaults to empty (new session / startup). Pass the previous map
         only when intentionally preserving soft-confirm trust across rebinds.
+        *access_grants* seeds session directory grants (empty clears them).
         """
         grant_map = dict(grants or {})
         store = MemoryViewStore({"todo": self.todo_stack.to_raw(), "grants": dict(grant_map)})
@@ -158,7 +193,9 @@ class ReplState:
             data=session_data_view(store=store),
             todo=self.todo_stack,
             on_todo_change=self._todo_on_change,
+            on_access_change=self._on_access_change,
             grants=grant_map,
+            access_grants=dict(access_grants or {}),
         )
 
     def _bind_todo_tools(self) -> None:
@@ -200,6 +237,67 @@ class ReplState:
         if hasattr(self, "agent"):
             self.agent.todo_stack = self.todo_stack
 
+    def _on_access_change(self) -> None:
+        """Schedule memory persist for live directory-access grants."""
+        import asyncio
+
+        if self.session_id is None:
+            return
+        try:
+            loop = asyncio.get_running_loop()
+        except RuntimeError:
+            return
+        task = loop.create_task(self.persist_access_grants())
+        self._todo_persist_tasks.add(task)
+        task.add_done_callback(self._todo_persist_tasks.discard)
+
+    async def persist_access_grants(self) -> None:
+        """Write live session directory grants to the active session row."""
+        if self.session_id is None:
+            return
+        payload = {str(path): mode.name.lower() for path, mode in self.session_state.access_grants.items()}
+        _ = await self.memory.update_session_access_grants(self.session_id, payload)
+
+    async def load_access_grants(self) -> None:
+        """Load durable session directory grants into the live map (replace)."""
+        self.session_state.access_grants.clear()
+        if self.session_id is None:
+            return
+        raw = await self.memory.get_session_access_grants(self.session_id)
+        self.session_state.access_grants.update(_parsed_access_grants(raw))
+
+    def directory_access_confirm_hook(
+        self,
+        path: Path,
+        mode: AccessMode,
+        reason: str,
+        timeout_seconds: float,
+    ) -> AccessDecision | str | None:
+        """Directory-access confirm: YOLO/``--yes`` auto-approves, else ask."""
+        from plyngent.cli.limits import prompt_directory_access_confirm
+        from plyngent.tools.access import AccessDecision as Decision
+
+        if self.effective_yolo() != "off":
+            return Decision(mode, persist=False)
+        return prompt_directory_access_confirm(path, mode, reason, timeout_seconds)
+
+    def _install_config_access(self) -> None:
+        """Install ``[agent].allow_paths`` static grants on the policy bag."""
+        import click
+
+        from plyngent.tools.access import set_config_access
+
+        _applied, skipped = set_config_access(
+            self.config.agent_config.allow_paths,
+            instance=self.instance_state,
+        )
+        if skipped:
+            click.secho(
+                f"warning: ignored allow_paths entries (missing path or bad mode): {', '.join(skipped)}",
+                fg="yellow",
+                err=True,
+            )
+
     def _tool_registry(self) -> ToolRegistry | None:
         if not self.tools_enabled:
             return None
@@ -215,6 +313,11 @@ class ReplState:
             plugins_cfg.enable,
             disable=plugins_cfg.disable,
         )
+        if self.mcp_manager is not None:
+            from plyngent.tools.mcp import register_mcp_tools
+
+            # Connections were started by the host; registration is sync-only.
+            _ = register_mcp_tools(self.mcp_manager, self.config.mcp_config)
         # Local surface: builtins + allowlisted plugins (import registers into catalog).
         tools = catalog.select(surface="local")
         yolo = self.effective_yolo() != "off"
@@ -229,16 +332,30 @@ class ReplState:
             session_state=self.session_state,
         )
 
+    def _mcp_instructions_text(self) -> str:
+        """Compose connected MCP servers' initialize ``instructions`` into one block.
+
+        Only meaningful when tools are on (MCP tools are registered under the
+        same condition); the text is attributed per server so the model can
+        weigh its provenance. Gated by ``[agent] mcp_instructions`` in callers.
+        """
+        if self.mcp_manager is None or not self.tools_enabled:
+            return ""
+        parts = [f"MCP server {name!r} instructions:\n{text}" for name, text in self.mcp_manager.instructions()]
+        return "\n\n".join(parts)
+
     def _make_agent(self) -> ChatAgent:
-        from plyngent.cli.limits import prompt_continue_limit_async
+        from plyngent.cli.limits import auto_continue_enabled, prompt_continue_limit_async
         from plyngent.config import compose_agent_system_content
 
         agent_cfg = self.config.agent_config
+        mcp_text = self._mcp_instructions_text() if agent_cfg.mcp_instructions else ""
         system_prompt = compose_agent_system_content(
             agent_cfg.system_prompt,
             agent_cfg.tool_directives,
+            mcp_text,
         )
-        on_limit = prompt_continue_limit_async if self.interactive_limits else None
+        on_limit = prompt_continue_limit_async if (self.interactive_limits or auto_continue_enabled()) else None
         peak = 0
         band = 0
         last_req = None
@@ -552,6 +669,7 @@ class ReplState:
         return False
 
     async def new_session(self, name: str = "chat") -> None:
+        self._reset_limit_auto_continue()
         session = await self.memory.create_session(
             name=name,
             workspace=self.workspace,
@@ -590,6 +708,7 @@ class ReplState:
         """Load a session; on workspace mismatch, prompt keep / rebind / abort."""
         from plyngent.cli.limits import prompt_workspace_mismatch
 
+        self._reset_limit_auto_continue()
         row = await self.memory.get_session(session_id)
         if row is None:
             msg = f"session not found: {session_id}"
@@ -623,9 +742,11 @@ class ReplState:
             self.agent = self._make_agent()
         await self.agent.load_history()
         await self.load_todo_stack()
+        await self.load_access_grants()
 
     async def resume_latest_or_new(self, name: str = "chat") -> str:
         """Resume most recently updated session for this workspace, or create one."""
+        self._reset_limit_auto_continue()
         latest = await self.memory.get_latest_session(workspace=self.workspace)
         if latest is None:
             await self.new_session(name=name)
@@ -638,6 +759,7 @@ class ReplState:
             self.agent = self._make_agent()
         await self.agent.load_history()
         await self.load_todo_stack()
+        await self.load_access_grants()
         _ = await self.memory.touch_session(latest.sid)
         return "resume"
 

src/plyngent/config/__init__.py

@@ -13,6 +13,8 @@ from .models import DatabaseConfig as DatabaseConfig
 from .models import DeepSeekConvention as DeepSeekConvention
 from .models import DeepseekProvider as DeepseekProvider
 from .models import HttpTimeoutConfig as HttpTimeoutConfig
+from .models import McpConfig as McpConfig
+from .models import McpServerConfig as McpServerConfig
 from .models import ModelConfig as ModelConfig
 from .models import NetworkingConfig as NetworkingConfig
 from .models import OpenAICompatibleProvider as OpenAICompatibleProvider

src/plyngent/config/models.py

@@ -10,6 +10,9 @@ from msgspec import Struct, field
 #                           ``https://api.deepseek.com/anthropic``)
 type DeepSeekConvention = Literal["", "openai", "anthropic", "responses"]
 
+# Static directory pre-allow mode for ``[agent].allow_paths`` (path → mode).
+type AllowPathMode = Literal["read", "write", "exec"]
+
 # Built-in persona when ``[agent].system_prompt`` is omitted.
 # Set ``system_prompt = ""`` to omit the persona block only.
 # Override with a multi-line TOML literal (prefer ''' so nested " is fine).
@@ -23,6 +26,8 @@ DEFAULT_TOOL_DIRECTIVES = """\
 ### Workspace
 - Explore with `tree`/`listdir`/`glob_paths`/`grep_files`/`read_file` when unsure.
 - Stay under the workspace (or a path from `new_temporary_workspace`). Respect path denylists.
+- Need a path outside the workspace? Call `request_directory_access` \
+(human approves; denylists apply) instead of retrying an escaped path.
 
 ### Files
 - Prefer file tools over shell. `edit_replace` fails usually means a bad match — \
@@ -70,19 +75,15 @@ call `todo_clear` (or pop finished TOP groups) so no hygiene noise is left behin
 """
 
 
-def compose_agent_system_content(
-    system_prompt: str,
-    tool_directives: str,
-) -> str | None:
-    """Join persona + tool playbook into one system body, or ``None`` if both empty.
+def compose_agent_system_content(*parts: str) -> str | None:
+    """Join persona + tool playbook + extra blocks into one system body.
 
-    Non-empty parts are stripped and joined with a blank line. Either field may
-    be ``""`` to disable that part while keeping the other.
+    Returns ``None`` when every part is empty. Non-empty parts are stripped and
+    joined with a blank line. Any part may be ``""`` to disable that block
+    (e.g. ``system_prompt = ""`` keeps the tool playbook).
     """
-    parts = [part.strip() for part in (system_prompt, tool_directives) if part and part.strip()]
-    if not parts:
-        return None
-    return "\n\n".join(parts)
+    joined = "\n\n".join(part.strip() for part in parts if part and part.strip())
+    return joined or None
 
 
 class DatabaseConfig(Struct, omit_defaults=True):
@@ -106,10 +107,19 @@ class AgentConfig(Struct, omit_defaults=True):
     system_prompt: str = DEFAULT_SYSTEM_PROMPT
     # Tool how-to (omit → DEFAULT_TOOL_DIRECTIVES; "" disables playbook only).
     tool_directives: str = DEFAULT_TOOL_DIRECTIVES
+    # Fold connected MCP servers' initialize ``instructions`` (usage guidance)
+    # into the agent system prompt when tools are on. false = ignore server text.
+    mcp_instructions: bool = True
     max_tool_result_chars: int = 32_000
     parallel_tools: bool = True
     confirm_destructive: bool = True
     path_denylist: list[str] = field(default_factory=list)
+    # Static directory pre-allow (resolved path → mode); never prompts.
+    # Denylist still applies, and the path must exist when chat starts.
+    allow_paths: dict[str, AllowPathMode] = field(default_factory=dict)
+    # Auto-raise tool/PTY limits without prompting (same as answering ``yyy``);
+    # process-wide, so every turn skips the limit confirm.
+    auto_continue_limits: bool = False
     max_context_tokens: int = 200_000
 
     # How to inject todo stack nags into model context (see agent/todo_nag.py).
@@ -143,6 +153,44 @@ class PluginsConfig(Struct, omit_defaults=True):
     disable: list[str] = field(default_factory=list)
 
 
+class McpServerConfig(Struct, omit_defaults=True):
+    """One MCP server definition (stdio transport today).
+
+    TOML example::
+
+        [mcp.servers.docs]
+        command = "npx"
+        args = ["-y", "@modelcontextprotocol/server-filesystem", "/tmp"]
+        env = { RUST_LOG = "info" }
+        # cwd = "/path"            # spawn working directory (empty = inherit)
+        # timeout = 30.0            # per-request timeout in seconds
+        # read_only = true          # mark every tool READ_ONLY (safe side turns)
+
+    ``url`` is reserved for the streamable-HTTP transport; empty = stdio.
+    A defined server is connected unless its name appears in ``[mcp].disable``.
+    """
+
+    command: str = ""
+    args: list[str] = field(default_factory=list)
+    env: dict[str, str] = field(default_factory=dict)
+    cwd: str = ""
+    timeout: float = 30.0
+    read_only: bool = False
+    url: str = ""
+
+
+class McpConfig(Struct, omit_defaults=True):
+    """Model Context Protocol servers exposed as agent tools.
+
+    Defining a server under ``[mcp.servers.<name>]`` is the opt-in; tools are
+    namespaced ``mcp__<server>__<tool>`` and registered with LOCAL tags. Names
+    in ``disable`` stay disconnected even when defined.
+    """
+
+    servers: dict[str, McpServerConfig] = field(default_factory=dict)
+    disable: list[str] = field(default_factory=list)
+
+
 class NetworkingConfig(Struct, omit_defaults=True):
     """Host-side network policy for tools such as ``fetch``.
 

src/plyngent/config/store.py

@@ -9,6 +9,7 @@ import tomlkit
 from .models import (
     AgentConfig,
     DatabaseConfig,
+    McpConfig,
     ModelConfig,
     NetworkingConfig,
     PluginsConfig,
@@ -56,6 +57,29 @@ def _parse_networking(raw: dict[str, object]) -> NetworkingConfig:
         return NetworkingConfig()
 
 
+def _parse_mcp(raw: dict[str, object]) -> McpConfig:
+    """Parse the ``[mcp]`` section, falling back to defaults.
+
+    Unknown keys (typos like ``cmds``) are rejected the same way as providers:
+    a malformed section silently degrades to "no MCP servers" instead of a
+    half-parsed one.
+    """
+    try:
+        config = msgspec.convert(raw, McpConfig)
+    except msgspec.ValidationError:
+        return McpConfig()
+    known = {"servers", "disable"}
+    if set(raw) - known:
+        return McpConfig()
+    known_server = {"command", "args", "env", "cwd", "timeout", "read_only", "url"}
+    servers_raw = cast("dict[str, object]", raw.get("servers", {}))
+    for name, raw_entry in servers_raw.items():
+        entry = cast("dict[str, object]", raw_entry)
+        if not isinstance(raw_entry, dict) or not name.strip() or set(entry) - known_server:
+            return McpConfig()
+    return config
+
+
 def _parse_providers(
     document: tomlkit.TOMLDocument,
 ) -> tuple[dict[str, Provider], dict[str, object], dict[str, Provider]]:
@@ -125,6 +149,7 @@ class ConfigStore:
     _agent: AgentConfig
     _plugins: PluginsConfig
     _networking: NetworkingConfig
+    _mcp: McpConfig
     _providers: dict[str, Provider]
     _bad_providers: dict[str, object]
     _recoverable_providers: dict[str, Provider]
@@ -137,6 +162,7 @@ class ConfigStore:
         self._agent = _parse_agent(cast("dict[str, object]", raw.get("agent", {})))
         self._plugins = _parse_plugins(cast("dict[str, object]", raw.get("plugins", {})))
         self._networking = _parse_networking(cast("dict[str, object]", raw.get("networking", {})))
+        self._mcp = _parse_mcp(cast("dict[str, object]", raw.get("mcp", {})))
         self._providers, self._bad_providers, self._recoverable_providers = _parse_providers(document)
 
     @property
@@ -187,6 +213,13 @@ class ConfigStore:
         """Typed networking section (e.g. Fake-IP SSRF exemptions)."""
         return self._networking
 
+    # -- mcp (read-only) --
+
+    @property
+    def mcp_config(self) -> McpConfig:
+        """Typed MCP section (server definitions + disable list)."""
+        return self._mcp
+
     def set_plugins_enable(self, names: Sequence[str]) -> PluginsConfig:
         """Replace the plugin enable list (in-memory; call :meth:`write` to persist)."""
         cleaned = [name.strip() for name in names if name.strip()]
@@ -390,6 +423,7 @@ class ConfigStore:
         self._agent = _parse_agent(cast("dict[str, object]", raw.get("agent", {})))
         self._plugins = _parse_plugins(cast("dict[str, object]", raw.get("plugins", {})))
         self._networking = _parse_networking(cast("dict[str, object]", raw.get("networking", {})))
+        self._mcp = _parse_mcp(cast("dict[str, object]", raw.get("mcp", {})))
         self._providers, self._bad_providers, self._recoverable_providers = _parse_providers(self._document)
 
     # -- internal sync helpers --

src/plyngent/memory/database/schema.py

@@ -34,6 +34,8 @@ class Session(PlyngentBase):
     model: Mapped[str | None] = mapped_column(String(256), nullable=True)
     # Todo/task stack JSON for multi-step sub-tasks (optional).
     todo_stack: Mapped[dict[str, object] | None] = mapped_column(JSON(), nullable=True)
+    # Directory-access grants approved for this session (resolved path → mode).
+    access_grants: Mapped[dict[str, str] | None] = mapped_column(JSON(), nullable=True)
     # Last model request context size (API prompt_tokens preferred).
     last_prompt_tokens: Mapped[int | None] = mapped_column(nullable=True)
     peak_prompt_tokens: Mapped[int | None] = mapped_column(nullable=True)

src/plyngent/memory/database/store.py

@@ -241,6 +241,31 @@ class MemoryStore:
             await session.refresh(row)
             return row
 
+    async def get_session_access_grants(self, sid: int) -> dict[str, str]:
+        """Return stored directory-access grants (resolved path → mode)."""
+        async with self._session_factory() as session:
+            row = await session.get(Session, sid)
+            if row is None:
+                msg = f"session not found: {sid}"
+                raise ValueError(msg)
+            raw = row.access_grants
+            if raw is None:
+                return {}
+            return {str(k): str(v) for k, v in cast("dict[object, object]", raw).items()}
+
+    async def update_session_access_grants(self, sid: int, grants: Mapping[str, str]) -> Session:
+        """Persist directory-access grants for a session (empty clears)."""
+        async with self._session_factory() as session:
+            row = await session.get(Session, sid)
+            if row is None:
+                msg = f"session not found: {sid}"
+                raise ValueError(msg)
+            row.access_grants = dict(grants)
+            row.updated_at = datetime.now(UTC)
+            await session.commit()
+            await session.refresh(row)
+            return row
+
     async def update_session_context_usage(
         self,
         sid: int,
@@ -400,18 +425,30 @@ def _migrate_session_v3(sync_conn: object, columns: set[str]) -> None:
         _ = sync_conn.execute(text("ALTER TABLE session ADD COLUMN reminder_last_band INTEGER"))
 
 
+def _migrate_session_v4(sync_conn: object, columns: set[str]) -> None:
+    """Post-v0.5.0: add ``access_grants`` JSON for session directory-access grants."""
+    from sqlalchemy.engine import Connection
+
+    if not isinstance(sync_conn, Connection):
+        return
+    if "access_grants" not in columns:
+        _ = sync_conn.execute(text("ALTER TABLE session ADD COLUMN access_grants JSON"))
+
+
 # Latest schema version this build knows. Bump (and append a step to
 # _SCHEMA_MIGRATIONS) when a new release adds or changes columns.
-_SCHEMA_VERSION = 3
+_SCHEMA_VERSION = 4
 
 # Ordered (version, step) pairs. Each step receives the current ``session``
 # column set (read once) and adds only its own missing columns, so it is
 # idempotent for DBs that were upgraded incrementally without a version stamp.
-# Version 1 shipped in v0.1.0, version 2 in v0.1.2, version 3 post-v0.2.0.
+# Version 1 shipped in v0.1.0, version 2 in v0.1.2, version 3 post-v0.2.0,
+# version 4 post-v0.5.0.
 _SCHEMA_MIGRATIONS: tuple[tuple[int, MigrationStep], ...] = (
     (1, _migrate_session_v1),
     (2, _migrate_session_v2),
     (3, _migrate_session_v3),
+    (4, _migrate_session_v4),
 )
 
 

src/plyngent/runtime/__init__.py

@@ -1,5 +1,11 @@
+from plyngent.config.models import McpConfig as McpConfig
+
 from .client_factory import InvalidHttpTimeoutError as InvalidHttpTimeoutError
 from .client_factory import ProviderNotSupportedError as ProviderNotSupportedError
 from .client_factory import create_client as create_client
 from .client_factory import normalize_http_timeout as normalize_http_timeout
 from .client_factory import provider_to_openai_config as provider_to_openai_config
+from .mcp_client import McpConnectionError as McpConnectionError
+from .mcp_client import McpManager as McpManager
+from .mcp_client import McpServerConnection as McpServerConnection
+from .mcp_client import McpTool as McpTool

src/plyngent/runtime/mcp_client.py

@@ -0,0 +1,383 @@
+"""MCP client: Model Context Protocol over stdio (newline-delimited JSON-RPC).
+
+One :class:`McpServerConnection` owns one spawned server subprocess and its
+initialize handshake. :class:`McpManager` owns all configured connections for
+the process: start, tool listing, tool calls, reconnect, shutdown.
+"""
+
+from __future__ import annotations
+
+import asyncio
+import importlib.metadata
+import json
+import os
+from collections import deque
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, cast
+
+if TYPE_CHECKING:
+    from plyngent.config.models import McpConfig, McpServerConfig
+
+MCP_PROTOCOL_VERSION = "2025-06-18"
+MCP_CLIENT_NAME = "plyngent"
+DEFAULT_MCP_TIMEOUT = 30.0
+_STDERR_TAIL_LINES = 32
+_CLOSE_GRACE_SECONDS = 2.0
+_MAX_TOOL_PAGES = 1024
+
+type Json = dict[str, object]
+
+
+def _json_dict(raw: object) -> Json:
+    """Narrow an untyped JSON payload to a string-keyed object mapping."""
+    return cast("Json", raw) if isinstance(raw, dict) else {}
+
+
+def _json_list(raw: object) -> list[object]:
+    """Narrow an untyped JSON payload to a list of objects."""
+    return cast("list[object]", raw) if isinstance(raw, list) else []
+
+
+def _client_version() -> str:
+    try:
+        return importlib.metadata.version("plyngent")
+    except importlib.metadata.PackageNotFoundError:
+        return "0.0.0"
+
+
+class McpConnectionError(RuntimeError):
+    """Server process failed to spawn, handshake, or answer in time."""
+
+
+@dataclass(frozen=True, slots=True)
+class McpTool:
+    """One tool advertised by a server (``tools/list`` entry)."""
+
+    name: str
+    description: str
+    input_schema: Json
+
+    @classmethod
+    def from_raw(cls, raw: object) -> McpTool:
+        entry = _json_dict(raw)
+        return cls(
+            name=str(entry.get("name", "")),
+            description=str(entry.get("description", "") or ""),
+            input_schema=_json_dict(entry.get("inputSchema")) or {"type": "object"},
+        )
+
+
+def _format_content(result: Json) -> str:
+    """Flatten a ``tools/call`` result payload into model-facing text."""
+    parts: list[str] = []
+    for item in _json_list(result.get("content")):
+        entry = _json_dict(item)
+        kind = str(entry.get("type", ""))
+        if kind == "text":
+            text = entry.get("text")
+            if isinstance(text, str):
+                parts.append(text)
+        elif kind == "resource":
+            parts.append(f"[resource] {json.dumps(entry, ensure_ascii=False)}")
+        else:
+            mime = entry.get("mimeType", "?")
+            parts.append(f"[{kind or 'unknown'}: {mime}]")
+    return "\n".join(parts)
+
+
+class McpServerConnection:
+    """One server subprocess with an active MCP session (stdio transport)."""
+
+    name: str
+    error: str | None
+    tools: list[McpTool]
+    tools_stale: bool
+    # Server usage guidance from the initialize result (InitializeResult.instructions).
+    instructions: str | None
+
+    _config: McpServerConfig
+    _proc: asyncio.subprocess.Process | None
+    _reader_task: asyncio.Task[None] | None
+    _pending: dict[int, asyncio.Future[Json]]
+    _next_id: int
+    _stderr_tail: deque[str]
+
+    def __init__(self, name: str, config: McpServerConfig) -> None:
+        self.name = name
+        self._config = config
+        self._proc = None
+        self._reader_task = None
+        self._pending = {}
+        self._next_id = 1
+        self._stderr_tail = deque(maxlen=_STDERR_TAIL_LINES)
+        self.error = None
+        self.tools = []
+        self.tools_stale = False
+        self.instructions = None
+
+    @property
+    def status(self) -> str:
+        if self.error is not None:
+            return f"error: {self.error}"
+        if self._proc is not None:
+            return "connected (tools changed; /mcp reconnect)" if self.tools_stale else "connected"
+        return "not started"
+
+    @property
+    def connected(self) -> bool:
+        return self._proc is not None and self.error is None
+
+    def stderr_tail(self) -> list[str]:
+        return list(self._stderr_tail)
+
+    async def start(self) -> None:
+        """Spawn the server process and run the initialize handshake."""
+        if self._proc is not None:
+            return
+        try:
+            self._proc = await asyncio.create_subprocess_exec(
+                self._config.command,
+                *self._config.args,
+                stdin=asyncio.subprocess.PIPE,
+                stdout=asyncio.subprocess.PIPE,
+                stderr=asyncio.subprocess.PIPE,
+                env=os.environ | self._config.env,
+                cwd=self._config.cwd or None,
+            )
+        except (OSError, ValueError) as exc:
+            self.error = f"spawn {self._config.command!r}: {exc}"
+            self._proc = None
+            return
+        self._reader_task = asyncio.create_task(self._read_loop())
+        try:
+            await self._initialize()
+            self.tools = await self.list_tools()
+        except (McpConnectionError, TimeoutError) as exc:
+            self.error = f"initialize: {exc}"
+            await self.aclose()
+
+    async def aclose(self) -> None:
+        """Terminate the server subprocess and fail pending requests."""
+        proc = self._proc
+        self._proc = None
+        if self._reader_task is not None:
+            _ = self._reader_task.cancel()
+            self._reader_task = None
+        if proc is not None and proc.returncode is None:
+            _ = proc.terminate()
+            try:
+                _ = await asyncio.wait_for(proc.wait(), _CLOSE_GRACE_SECONDS)
+            except TimeoutError:
+                proc.kill()
+                _ = await proc.wait()
+        for future in self._pending.values():
+            if not future.done():
+                future.set_exception(McpConnectionError("connection closed"))
+        self._pending.clear()
+
+    async def _read_loop(self) -> None:
+        proc = self._proc
+        if proc is None or proc.stdout is None or proc.stderr is None:
+            return
+        stderr_task = asyncio.create_task(self._drain_stderr(proc.stderr))
+        try:
+            while True:
+                line = await proc.stdout.readline()
+                if not line:
+                    break
+                self._dispatch(line)
+        finally:
+            _ = stderr_task.cancel()
+            for future in self._pending.values():
+                if not future.done():
+                    future.set_exception(McpConnectionError("server closed the stream"))
+            self._pending.clear()
+
+    async def _drain_stderr(self, stderr: asyncio.StreamReader) -> None:
+        while True:
+            line = await stderr.readline()
+            if not line:
+                return
+            self._stderr_tail.append(line.decode(errors="replace").rstrip())
+
+    def _dispatch(self, line: bytes) -> None:
+        try:
+            payload = _json_dict(cast("object", json.loads(line)))
+        except json.JSONDecodeError:
+            return
+        message_id = payload.get("id")
+        if message_id is not None:
+            if isinstance(message_id, bool) or not isinstance(message_id, (int, str)):
+                return
+            request_id = int(message_id)
+            future = self._pending.pop(request_id, None)
+            if future is None or future.done():
+                return
+            error = payload.get("error")
+            if error is not None:
+                err = _json_dict(error)
+                detail = str(err.get("message", "unknown error")) if err else str(error)
+                future.set_exception(McpConnectionError(detail))
+            else:
+                future.set_result(_json_dict(payload.get("result")))
+            return
+        # Notifications carry no id; only tool-list changes matter to the host.
+        if payload.get("method") == "notifications/tools/list_changed":
+            self.tools_stale = True
+
+    def _send(self, payload: Json) -> None:
+        proc = self._proc
+        stdin = proc.stdin if proc is not None else None
+        if stdin is None:
+            msg = "server process is not running"
+            raise McpConnectionError(msg)
+        _ = stdin.write(json.dumps(payload, ensure_ascii=False).encode() + b"\n")
+
+    async def _request(self, method: str, params: Json | None = None) -> Json:
+        timeout = self._config.timeout or DEFAULT_MCP_TIMEOUT
+        future: asyncio.Future[Json] = asyncio.get_running_loop().create_future()
+        request_id = self._next_id
+        self._next_id += 1
+        self._pending[request_id] = future
+        payload: Json = {"jsonrpc": "2.0", "id": request_id, "method": method}
+        if params is not None:
+            payload["params"] = params
+        try:
+            self._send(payload)
+        except McpConnectionError:
+            _ = self._pending.pop(request_id, None)
+            raise
+        try:
+            return await asyncio.wait_for(future, timeout)
+        except TimeoutError:
+            _ = self._pending.pop(request_id, None)
+            msg = f"{method} timed out after {timeout}s"
+            raise McpConnectionError(msg) from None
+
+    async def _notify(self, method: str, params: Json | None = None) -> None:
+        payload: Json = {"jsonrpc": "2.0", "method": method}
+        if params is not None:
+            payload["params"] = params
+        self._send(payload)
+
+    async def _initialize(self) -> None:
+        result = await self._request(
+            "initialize",
+            {
+                "protocolVersion": MCP_PROTOCOL_VERSION,
+                "capabilities": {},
+                "clientInfo": {"name": MCP_CLIENT_NAME, "version": _client_version()},
+            },
+        )
+        # Optional server usage guidance (MCP spec: InitializeResult.instructions).
+        # Hosts surface this to the model when the server's tools are in play.
+        instructions = result.get("instructions")
+        self.instructions = instructions.strip() if isinstance(instructions, str) and instructions.strip() else None
+        await self._notify("notifications/initialized")
+
+    async def list_tools(self) -> list[McpTool]:
+        """Fetch the full tool list, following ``nextCursor`` pagination."""
+        tools: list[McpTool] = []
+        cursor: str | None = None
+        for _ in range(_MAX_TOOL_PAGES):
+            params: Json = {} if cursor is None else {"cursor": cursor}
+            result = await self._request("tools/list", params)
+            tools.extend(McpTool.from_raw(item) for item in _json_list(result.get("tools")))
+            next_cursor = result.get("nextCursor")
+            if not isinstance(next_cursor, str) or not next_cursor:
+                return tools
+            cursor = next_cursor
+        return tools
+
+    async def call_tool(self, name: str, arguments: Json) -> str:
+        """Run ``tools/call`` and return the flattened text result.
+
+        Tool-level failures (``isError``) come back as ``error: …`` text, not
+        exceptions: the protocol round-trip itself succeeded.
+        """
+        result = await self._request("tools/call", {"name": name, "arguments": arguments})
+        text = _format_content(result)
+        if result.get("isError") is True:
+            return f"error: {text or 'tool reported failure without content'}"
+        return text
+
+
+class McpManager:
+    """All configured MCP server connections for this process."""
+
+    _config: McpConfig
+    _connections: dict[str, McpServerConnection]
+
+    def __init__(self, config: McpConfig) -> None:
+        self._config = config
+        self._connections = {}
+
+    def enabled_servers(self) -> dict[str, McpServerConfig]:
+        """Configured servers minus the ``disable`` list, in config order."""
+        disabled = {name.strip() for name in self._config.disable}
+        return {name: cfg for name, cfg in self._config.servers.items() if name not in disabled}
+
+    async def ensure_started(self) -> None:
+        """Connect every enabled server that has no live connection yet."""
+        for name, cfg in self.enabled_servers().items():
+            connection = self._connections.get(name)
+            if connection is not None and connection.connected:
+                continue
+            if connection is not None:
+                await connection.aclose()
+            connection = McpServerConnection(name, cfg)
+            self._connections[name] = connection
+            await connection.start()
+
+    async def restart(self, config: McpConfig) -> None:
+        """Drop every connection and adopt a new config (e.g. /mcp reconnect)."""
+        await self.aclose()
+        self._config = config
+
+    async def aclose(self) -> None:
+        for connection in self._connections.values():
+            await connection.aclose()
+        self._connections.clear()
+
+    def statuses(self) -> list[tuple[str, str, int]]:
+        """(server, status, tool_count) rows for diagnostics surfaces."""
+        rows: list[tuple[str, str, int]] = []
+        for name in self.enabled_servers():
+            connection = self._connections.get(name)
+            if connection is None:
+                rows.append((name, "not started", 0))
+            else:
+                rows.append((name, connection.status, len(connection.tools)))
+        return rows
+
+    def instructions(self) -> list[tuple[str, str]]:
+        """(server, text) initialize ``instructions`` for every connected server.
+
+        Only non-empty guidance is returned, in config order. Hosts may fold
+        these into the agent system context (see cli.state.ReplState).
+        """
+        rows: list[tuple[str, str]] = []
+        for name in self.enabled_servers():
+            connection = self._connections.get(name)
+            if connection is not None and connection.connected:
+                text = (connection.instructions or "").strip()
+                if text:
+                    rows.append((name, text))
+        return rows
+
+    def connections(self) -> list[McpServerConnection]:
+        return list(self._connections.values())
+
+    async def refresh_tools(self) -> None:
+        """Re-run tools/list on every connected server."""
+        for connection in self._connections.values():
+            if connection.connected:
+                connection.tools = await connection.list_tools()
+                connection.tools_stale = False
+
+    async def call(self, server: str, tool: str, arguments: Json) -> str:
+        connection = self._connections.get(server)
+        if connection is None or not connection.connected:
+            msg = f"server {server!r} is not connected"
+            raise McpConnectionError(msg)
+        return await connection.call_tool(tool, arguments)

src/plyngent/tools/__init__.py

@@ -1,3 +1,17 @@
+from .access import ACCESS_TOOLS as ACCESS_TOOLS
+from .access import MAX_ACCESS_GRANTS as MAX_ACCESS_GRANTS
+from .access import AccessDecision as AccessDecision
+from .access import access_grant_rows as access_grant_rows
+from .access import active_grant_count as active_grant_count
+from .access import clear_process_access as clear_process_access
+from .access import clear_session_access as clear_session_access
+from .access import get_directory_access_confirm_hook as get_directory_access_confirm_hook
+from .access import grant_process_access as grant_process_access
+from .access import grant_session_access as grant_session_access
+from .access import request_directory_access as request_directory_access
+from .access import revoke_access as revoke_access
+from .access import set_config_access as set_config_access
+from .access import set_directory_access_confirm_hook as set_directory_access_confirm_hook
 from .catalog import ToolCatalog as ToolCatalog
 from .catalog import ToolSource as ToolSource
 from .catalog import catalog_scope as catalog_scope
@@ -66,6 +80,7 @@ from .workspace import (
     DEFAULT_COMMAND_DENYLIST as DEFAULT_COMMAND_DENYLIST,
 )
 from .workspace import DEFAULT_POLICY_CONFIRM_TIMEOUT_SECONDS as DEFAULT_POLICY_CONFIRM_TIMEOUT_SECONDS
+from .workspace import AccessMode as AccessMode
 from .workspace import WorkspaceError as WorkspaceError
 from .workspace import WorkspacePolicy as WorkspacePolicy
 from .workspace import active_workspace_policy as active_workspace_policy
@@ -74,12 +89,16 @@ from .workspace import check_command_allowed as check_command_allowed
 from .workspace import clear_policy_allowed_commands as clear_policy_allowed_commands
 from .workspace import clear_workspace_allowlist as clear_workspace_allowlist
 from .workspace import clear_workspace_root as clear_workspace_root
+from .workspace import denylist_match as denylist_match
 from .workspace import get_command_denylist as get_command_denylist
 from .workspace import get_path_denylist as get_path_denylist
 from .workspace import get_policy_confirm_timeout as get_policy_confirm_timeout
 from .workspace import get_workspace_root as get_workspace_root
 from .workspace import grant_policy_command as grant_policy_command
+from .workspace import granted_access_mode as granted_access_mode
 from .workspace import list_workspace_allowlist as list_workspace_allowlist
+from .workspace import mode_covers as mode_covers
+from .workspace import parse_access_mode as parse_access_mode
 from .workspace import pop_owned_temporary_workspaces as pop_owned_temporary_workspaces
 from .workspace import remove_workspace_allowlist as remove_workspace_allowlist
 from .workspace import resolve_path as resolve_path
@@ -88,3 +107,4 @@ from .workspace import set_path_denylist as set_path_denylist
 from .workspace import set_policy_confirm_hook as set_policy_confirm_hook
 from .workspace import set_policy_confirm_timeout as set_policy_confirm_timeout
 from .workspace import set_workspace_root as set_workspace_root
+from .workspace import within_workspace_roots as within_workspace_roots

src/plyngent/tools/access.py

@@ -0,0 +1,286 @@
+"""Directory-access grants: request tool plus config / session / process stores.
+
+A grant is one ``path → mode`` pair; its *source* is structural:
+
+- :attr:`WorkspacePolicy.config_allow` — static TOML pre-allow (never prompts),
+- :attr:`SessionState.access_grants` — human-approved for this session,
+- :attr:`WorkspacePolicy.yolo_allow` — ``--yes`` / YOLO auto-approval, process only.
+
+``resolve_path`` consults all three. Grants are a policy gate for path-resolving
+tools, **not** a sandbox: an ``exec`` grant (or any command) can reach the rest
+of the filesystem.
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import TYPE_CHECKING, NamedTuple
+
+from plyngent.agent import ToolTag, tool
+from plyngent.tools.context import get_session, require_session
+from plyngent.tools.workspace import (
+    AccessMode,
+    denylist_match,
+    get_policy_confirm_timeout,
+    granted_access_mode,
+    mode_covers,
+    parse_access_mode,
+    require_bound_instance,
+    within_workspace_roots,
+)
+
+if TYPE_CHECKING:
+    from collections.abc import Callable, Mapping
+
+    from plyngent.tools.context import InstanceState, SessionState
+
+# Max active grants across all three stores (bounds prompt/listing noise).
+MAX_ACCESS_GRANTS = 32
+
+_HOOK_KEY = "directory_access_confirm_hook"
+
+
+class AccessDecision(NamedTuple):
+    """Hook approval for one directory-access request.
+
+    ``mode`` is the granted level (may differ from the requested one);
+    ``persist`` is true for a session grant, false for a process-only grant.
+    """
+
+    mode: AccessMode
+    persist: bool = True
+
+
+type DirectoryAccessConfirmHook = Callable[[Path, AccessMode, str, float], AccessDecision | str | None]
+
+
+def get_directory_access_confirm_hook(instance: InstanceState | None = None) -> DirectoryAccessConfirmHook | None:
+    """Return the host-installed confirm hook for this instance, if any."""
+    inst = instance if instance is not None else require_bound_instance()
+    hook = inst.extras.get(_HOOK_KEY)
+    if hook is None or not callable(hook):
+        return None
+
+    def _as_hook(path: Path, mode: AccessMode, reason: str, timeout: float) -> AccessDecision | str | None:
+        result: object = hook(path, mode, reason, timeout)
+        if isinstance(result, AccessDecision | str):
+            return result
+        return None
+
+    return _as_hook
+
+
+def set_directory_access_confirm_hook(
+    hook: DirectoryAccessConfirmHook | None,
+    *,
+    instance: InstanceState | None = None,
+) -> None:
+    """Install (or clear) the confirm hook the CLI uses to ask the human."""
+    inst = instance if instance is not None else require_bound_instance()
+    inst.extras[_HOOK_KEY] = hook
+
+
+def _notify_access_change(session: SessionState | None) -> None:
+    """Fire the host's persist hook after the live session map changes."""
+    if session is not None and session.on_access_change is not None:
+        session.on_access_change()
+
+
+def grant_session_access(
+    path: Path | str,
+    mode: AccessMode,
+    *,
+    session: SessionState | None = None,
+) -> Path:
+    """Grant *mode* on *path* for the bound session; returns the resolved path."""
+    resolved = Path(path).expanduser().resolve()
+    sess = session if session is not None else require_session()
+    sess.access_grants[resolved] = mode
+    _notify_access_change(sess)
+    return resolved
+
+
+def grant_process_access(path: Path | str, mode: AccessMode) -> Path:
+    """Grant *mode* on *path* for this process only (``--yes``); never persisted."""
+    resolved = Path(path).expanduser().resolve()
+    require_bound_instance().workspace.yolo_allow[resolved] = mode
+    return resolved
+
+
+def clear_process_access(*, instance: InstanceState | None = None) -> None:
+    """Drop process-scoped (``--yes``) grants."""
+    inst = instance if instance is not None else require_bound_instance()
+    inst.workspace.yolo_allow.clear()
+
+
+def clear_session_access(*, session: SessionState | None = None) -> None:
+    """Drop live session grants (durable copy is cleared by the host)."""
+    sess = session if session is not None else get_session()
+    if sess is not None:
+        sess.access_grants.clear()
+        _notify_access_change(sess)
+
+
+def active_grant_count() -> int:
+    """Total live grants across config, session, and process stores."""
+    policy = require_bound_instance().workspace
+    total = len(policy.config_allow) + len(policy.yolo_allow)
+    session = get_session()
+    if session is not None:
+        total += len(session.access_grants)
+    return total
+
+
+def set_config_access(
+    entries: Mapping[str, str],
+    *,
+    instance: InstanceState | None = None,
+) -> tuple[list[Path], list[str]]:
+    """Install static TOML pre-allow entries on the instance policy bag.
+
+    Replaces any previous config grants. Returns ``(applied roots, skipped
+    keys)``; entries are skipped when the mode is unknown or the path does not
+    exist (the host warns about skipped keys).
+    """
+    inst = instance if instance is not None else require_bound_instance()
+    policy = inst.workspace
+    policy.config_allow.clear()
+    applied: list[Path] = []
+    skipped: list[str] = []
+    for raw_path, raw_mode in entries.items():
+        mode = parse_access_mode(raw_mode)
+        resolved: Path | None
+        try:
+            resolved = Path(raw_path).expanduser().resolve()
+        except OSError:
+            resolved = None
+        if mode is None or resolved is None or not resolved.exists():
+            skipped.append(raw_path)
+            continue
+        policy.config_allow[resolved] = mode
+        applied.append(resolved)
+    return applied, skipped
+
+
+def access_grant_rows(
+    *,
+    instance: InstanceState | None = None,
+    session: SessionState | None = None,
+) -> list[tuple[Path, AccessMode, str]]:
+    """``(path, mode, source)`` rows: session, then process, then config."""
+    inst = instance if instance is not None else require_bound_instance()
+    sess = session if session is not None else get_session()
+    rows: list[tuple[Path, AccessMode, str]] = []
+    if sess is not None:
+        rows.extend((path, mode, "session") for path, mode in sess.access_grants.items())
+    rows.extend((path, mode, "process") for path, mode in inst.workspace.yolo_allow.items())
+    rows.extend((path, mode, "config") for path, mode in inst.workspace.config_allow.items())
+    return rows
+
+
+def revoke_access(
+    path: Path | str,
+    *,
+    source: str,
+    instance: InstanceState | None = None,
+    session: SessionState | None = None,
+) -> bool:
+    """Remove the exact resolved *path* from one store; false if not present.
+
+    ``config`` grants are owned by ``[agent].allow_paths`` and are not removed
+    here (the caller should point the human at the config file).
+    """
+    resolved = Path(path).expanduser().resolve()
+    if source == "session":
+        sess = session if session is not None else get_session()
+        if sess is None or sess.access_grants.pop(resolved, None) is None:
+            return False
+        _notify_access_change(sess)
+        return True
+    if source == "process":
+        inst = instance if instance is not None else require_bound_instance()
+        return inst.workspace.yolo_allow.pop(resolved, None) is not None
+    return False
+
+
+def _resolve_target(path: str) -> Path | str:
+    """Resolve a requested path; return a model-facing error string on failure."""
+    try:
+        target = Path(path).expanduser().resolve()
+    except OSError as exc:
+        return f"error: cannot resolve path {path!r}: {exc}"
+    if not target.exists():
+        return f"error: path does not exist: {target}"
+    return target
+
+
+def _precheck_target(target: Path, requested: AccessMode) -> str | None:
+    """Return a short-circuit message when no prompt is needed, else ``None``."""
+    if requested is AccessMode.EXEC and not target.is_dir():
+        return f"error: exec access requires a directory: {target}"
+    matched = denylist_match(target, directory=target.is_dir())
+    if matched is not None:
+        return f"error: path denied by policy (matched {matched!r}); it can never be granted: {target}"
+    if within_workspace_roots(target):
+        return f"already accessible: {target} is inside the workspace"
+    granted = granted_access_mode(target)
+    if granted is not None and mode_covers(granted, requested):
+        return f"already granted: {target} ({granted.name.lower()})"
+    if active_grant_count() >= MAX_ACCESS_GRANTS:
+        return f"error: too many active access grants (max {MAX_ACCESS_GRANTS}); revoke some first"
+    return None
+
+
+def _apply_decision(target: Path, decision: AccessDecision | str | None, timeout: float) -> str:
+    """Record an approved grant or format the denial for the model."""
+    if isinstance(decision, AccessDecision):
+        if decision.persist and get_session() is not None:
+            _ = grant_session_access(target, decision.mode)
+            scope = "session"
+        else:
+            _ = grant_process_access(target, decision.mode)
+            scope = "process"
+        return (
+            f"access granted: {target} ({decision.mode.name.lower()}, {scope})\n"
+            "note: the path denylist still applies; the human can revoke with /grants"
+        )
+    if isinstance(decision, str) and decision.strip():
+        return f"error: access to {target} denied by user; user comment: {decision.strip()}"
+    return f"error: access to {target} denied (declined or timed out after {timeout:g}s)"
+
+
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.SESSION_STATE)
+async def request_directory_access(path: str, reason: str = "", mode: str = "read") -> str:
+    """Request human approval to use a directory (or exact file) outside the workspace.
+
+    Call this instead of retrying a path that failed with ``path escapes
+    workspace root``. ``mode`` is ``read`` (inspect files), ``write`` (also
+    modify files) or ``exec`` (also use it as ``run_argv`` / PTY cwd); the human
+    may approve a different level. Approval lasts for the session (or for this
+    process when ``--yes`` auto-approves). Paths matching the configured
+    denylist can never be granted.
+    """
+    requested = parse_access_mode(mode)
+    if requested is None:
+        return f"error: invalid mode {mode!r} (use read, write, or exec)"
+    resolved = _resolve_target(path)
+    if isinstance(resolved, str):
+        return resolved
+    target = resolved
+    precheck = _precheck_target(target, requested)
+    if precheck is not None:
+        return precheck
+    hook = get_directory_access_confirm_hook()
+    if hook is None:
+        return f"error: access to {target} requires a human confirm (no confirm hook installed; denied)"
+    timeout = get_policy_confirm_timeout()
+    try:
+        decision = hook(target, requested, reason, timeout)
+    except Exception as exc:  # noqa: BLE001 — surface confirm failures to the model
+        return f"error: access confirm for {target} failed: {exc}"
+    return _apply_decision(target, decision, timeout)
+
+
+ACCESS_TOOLS = [
+    request_directory_access,
+]

src/plyngent/tools/catalog.py

@@ -12,7 +12,7 @@ from plyngent.agent.tools import ToolDefinition, ToolTag
 if TYPE_CHECKING:
     from collections.abc import Container, Generator
 
-type ToolSourceKind = Literal["builtin", "plugin"]
+type ToolSourceKind = Literal["builtin", "plugin", "mcp"]
 type ToolSurface = Literal["local", "public"]
 
 
@@ -29,8 +29,8 @@ class ToolSource:
     def __str__(self) -> str:
         if self.kind == "builtin":
             return "builtin"
-        plugin = self.plugin_id or "?"
-        return f"plugin:{plugin}"
+        id_part = self.plugin_id or "?"
+        return f"{self.kind}:{id_part}"
 
 
 @dataclass(frozen=True, slots=True)
@@ -152,6 +152,13 @@ class ToolCatalog:
     def clear(self) -> None:
         self._by_name.clear()
 
+    def purge_kind(self, kind: ToolSourceKind) -> int:
+        """Remove every entry registered from *kind*; return the count removed."""
+        doomed = [name for name, entry in self._by_name.items() if entry.source.kind == kind]
+        for name in doomed:
+            del self._by_name[name]
+        return len(doomed)
+
     def snapshot(self) -> dict[str, RegisteredTool]:
         return dict(self._by_name)
 
@@ -211,6 +218,7 @@ def _ensure_builtin_definitions_registered(catalog: ToolCatalog) -> None:
     import time (usually the process catalog). Test ``catalog_scope(empty=True)``
     overrides must still see builtins for ``default_tool_definitions``.
     """
+    from plyngent.tools.access import ACCESS_TOOLS
     from plyngent.tools.chat import CHAT_TOOLS
     from plyngent.tools.file import FILE_TOOLS
     from plyngent.tools.net import NET_TOOLS
@@ -219,6 +227,7 @@ def _ensure_builtin_definitions_registered(catalog: ToolCatalog) -> None:
     from plyngent.tools.vcs import VCS_TOOLS
 
     for definition in (
+        *ACCESS_TOOLS,
         *FILE_TOOLS,
         *PROCESS_TOOLS,
         *VCS_TOOLS,

src/plyngent/tools/chat/ask.py

@@ -4,7 +4,7 @@ from plyngent.agent import ToolTag, tool
 from plyngent.prompting import NonInteractiveError, ask_async
 
 
-@tool(name="ask_user_line", tags=ToolTag.LOCAL)
+@tool(name="ask_user_line", tags=ToolTag.LOCAL | ToolTag.READ_ONLY)
 async def ask_user(question: str, default: str = "") -> str:
     """Ask the human a free-form one-line question and return their answer.
 

src/plyngent/tools/chat/choose.py

@@ -36,7 +36,7 @@ def parse_options(options: list[object]) -> list[ChoiceOption]:
     return out
 
 
-@tool(name="ask_user_choice", tags=ToolTag.LOCAL)
+@tool(name="ask_user_choice", tags=ToolTag.LOCAL | ToolTag.READ_ONLY)
 async def choose_user(
     question: str,
     options: list[str] | list[dict[str, object]],

src/plyngent/tools/chat/form.py

@@ -46,7 +46,7 @@ def parse_fields(fields: list[dict[str, object]]) -> list[FormField]:
     return out
 
 
-@tool(name="ask_user_form", tags=ToolTag.LOCAL)
+@tool(name="ask_user_form", tags=ToolTag.LOCAL | ToolTag.READ_ONLY)
 async def form_user(
     title: str,
     fields: list[dict[str, object]],

src/plyngent/tools/chat/wait.py

@@ -1,20 +1,44 @@
 from __future__ import annotations
 
 import asyncio
+import re
+import sys
+
+from click import style
 
 from plyngent.agent import ToolTag, tool
 from plyngent.prompting import get_prompt_backend, read_line_with_timeout, run_prompt_async
 
-WAIT_PROMPT = "Waiting for {duration}s. Press Enter to disturb. Feel free to ship any reason before pressing Enter. "
+_ANSI_ESCAPE_RE = re.compile(r"\x1b\[[0-9;]*m")
 
 
-@tool(name="wait", tags=ToolTag.LOCAL)
+def _wait_prompt(duration: int, *, reason: str | None) -> str:
+    """Two-line wait prompt: status line, then the optional-reason input prompt.
+
+    ``read_line_with_timeout`` writes the prompt verbatim to stdout (no click
+    echo ANSI stripping), so styling is applied here and stripped when stdout
+    is not a TTY. On a terminal: cyan status, dimmed detail, yellow input
+    prompt; plain text otherwise (tests, redirected output).
+    """
+    status = style(f"Waiting for {duration}s", fg="cyan")
+    if reason:
+        status += style(f" ({reason})", fg="bright_black")
+    status += style(". Press Enter to disturb.", fg="bright_black")
+    input_prompt = style("Reason (optional): ", fg="yellow")
+    rendered = f"{status}\n{input_prompt}"
+    if not sys.stdout.isatty():
+        return _ANSI_ESCAPE_RE.sub("", rendered)
+    return rendered
+
+
+@tool(name="wait", tags=ToolTag.LOCAL | ToolTag.READ_ONLY)
 async def wait(duration: int, *, reason: str | None = None) -> str:
     """Wait ``duration`` seconds before continuing.
 
-    Interactive sessions show a line prompt: pressing Enter (optionally after
-    typing a reason) "disturbs" the wait so the turn continues immediately.
-    Non-interactive runs simply sleep the full duration.
+    Interactive sessions show a two-line prompt: a status line, then an
+    optional-reason input — pressing Enter (optionally after typing a reason)
+    "disturbs" the wait so the turn continues immediately. Non-interactive runs
+    simply sleep the full duration.
     """
     if duration < 0:
         return "error: duration must not be negative"
@@ -24,12 +48,7 @@ async def wait(duration: int, *, reason: str | None = None) -> str:
     if not backend.is_interactive():
         await asyncio.sleep(duration)
         return f"waited {duration}s"
-    prompt = WAIT_PROMPT.format(duration=duration)
-    if reason:
-        prompt = (
-            f"Waiting for {duration}s (reason: {reason}). Press Enter to disturb. "
-            "Feel free to ship any reason before pressing Enter. "
-        )
+    prompt = _wait_prompt(duration, reason=reason)
     line = await run_prompt_async(read_line_with_timeout, prompt, float(duration))
     if line is None:
         return f"waited {duration}s"

src/plyngent/tools/context.py

@@ -14,7 +14,7 @@ if TYPE_CHECKING:
     from pathlib import Path
 
     from plyngent.agent.todo_stack import TodoStack
-    from plyngent.tools.workspace import WorkspacePolicy
+    from plyngent.tools.workspace import AccessMode, WorkspacePolicy
 
 
 def _default_instance_data() -> PersistentDataView[Any]:
@@ -74,10 +74,15 @@ class SessionState:
     todo: TodoStack | None = None
     # Host hook after todo tools mutate (e.g. CLI memory persist).
     on_todo_change: Callable[[], None] | None = None
+    # Host hook after directory-access grants change (e.g. CLI memory persist).
+    on_access_change: Callable[[], None] | None = None
     # Soft-confirm grants live map: tool_name → True (Phase 1 key is tool name).
     # Durable copy lives under data["grants"] (see plyngent.tools.grants).
     grants: dict[str, bool] = field(default_factory=dict)
     extras: dict[str, Any] = field(default_factory=dict)
+    # Directory-access grants for this session (resolved path → mode). Config /
+    # process-scoped grants live on WorkspacePolicy; see plyngent.tools.access.
+    access_grants: dict[Path, AccessMode] = field(default_factory=dict)
 
     def has_grant(self, tool_name: str) -> bool:
         return bool(self.grants.get(tool_name))
@@ -137,6 +142,29 @@ def bind_session(state: SessionState | None) -> Generator[SessionState | None]:
         _session.reset(token)
 
 
+_read_only: ContextVar[bool] = ContextVar("plyngent_read_only_context", default=False)
+
+
+@contextmanager
+def read_only_context() -> Generator[None]:
+    """Mark the current context as read-only for tool execution.
+
+    Tools that may mutate depending on arguments (e.g. ``fetch`` with a
+    non-GET method) check :func:`is_read_only_context` and refuse to mutate
+    while it is set.
+    """
+    token = _read_only.set(True)
+    try:
+        yield
+    finally:
+        _read_only.reset(token)
+
+
+def is_read_only_context() -> bool:
+    """Whether tools currently run inside a read-only context."""
+    return _read_only.get()
+
+
 @contextmanager
 def bind_tool_context(
     *,

src/plyngent/tools/danger.py

@@ -4,7 +4,7 @@ import json
 import shlex
 from typing import TYPE_CHECKING, cast
 
-from plyngent.tools.workspace import WorkspaceError, resolve_path
+from plyngent.tools.workspace import AccessMode, WorkspaceError, resolve_path
 
 if TYPE_CHECKING:
     from collections.abc import Mapping, Sequence
@@ -140,7 +140,7 @@ def _write_file_reason(args: Mapping[str, object]) -> str | None:
     if not isinstance(path, str) or not path:
         return None
     try:
-        target = resolve_path(path)
+        target = resolve_path(path, required=AccessMode.WRITE)
     except WorkspaceError:
         # Path policy will fail later; no soft-confirm without a resolved target.
         return None
@@ -160,7 +160,7 @@ def _copy_path_reason(args: Mapping[str, object]) -> str | None:
     if not isinstance(dst, str) or not dst:
         return f"copy {src!r} → {dst!r} (overwrite)"
     try:
-        target = resolve_path(dst)
+        target = resolve_path(dst, required=AccessMode.WRITE)
     except WorkspaceError:
         return None
     if target.exists():

src/plyngent/tools/file/edit_lineno.py

@@ -2,8 +2,8 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
-from plyngent.agent import ToolTag, invalidate_lineno_read, lineno_read_lines, tool
-from plyngent.tools.workspace import resolve_path
+from plyngent.agent import ToolTag, lineno_read_lines, lineno_read_mtime, tool
+from plyngent.tools.workspace import AccessMode, resolve_path
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -60,10 +60,11 @@ def _unread_lines_in_range(
     """Lines in ``start_line..end_line`` that were not read with line numbers.
 
     Appending (``start_line == n + 1``) requires the last line to be read, so
-    line numbers stay truthful; the append point itself is not a line.
+    line numbers stay truthful; the append point itself is not a line. An empty
+    file (``n == 0``) has nothing to clobber, so appending needs no read.
     """
     if start_line == n + 1:
-        return [] if n in read_lines else [n]
+        return [] if n == 0 or n in read_lines else [n]
     return sorted(set(range(start_line, end_line + 1)) - read_lines)
 
 
@@ -77,6 +78,14 @@ def _append_after(target: Path, path: str, text: str, lines: list[str], new_cont
     return f"appended content after line {n} in {path}"
 
 
+def _excerpt(text: str, limit: int = 40) -> str:
+    """Collapse newlines and truncate for a one-line message excerpt."""
+    one = text.replace("\r\n", " ").replace("\n", " ")
+    if len(one) > limit:
+        return one[:limit] + "…"
+    return one
+
+
 def _replace_range(
     target: Path,
     path: str,
@@ -92,7 +101,11 @@ def _replace_range(
     new_lines = lines[: start_line - 1] + replacement + lines[end:]
     _ = target.write_text("".join(new_lines), encoding="utf-8")
     removed = end - start_line + 1
-    return f"replaced lines {start_line}-{end} ({removed} lines) with {len(replacement)} lines in {path}"
+    old_first = _excerpt(lines[start_line - 1].rstrip("\r\n"))
+    return (
+        f"replaced lines {start_line}-{end} ({removed} lines; first: {old_first!r}) "
+        f"with {len(replacement)} lines in {path}"
+    )
 
 
 @tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.YOLO)
@@ -101,7 +114,7 @@ async def edit_lineno(path: str, start_line: int, end_line: int, new_content: st
 
     ``new_content`` may be multi-line. Use an empty string to delete the range.
     """
-    target = resolve_path(path)
+    target = resolve_path(path, required=AccessMode.WRITE)
     if not target.is_file():
         return f"error: not a file: {path}"
 
@@ -111,18 +124,37 @@ async def edit_lineno(path: str, start_line: int, end_line: int, new_content: st
     if err is not None:
         return err
 
-    unread = _unread_lines_in_range(lineno_read_lines(str(target)), start_line, end_line, len(lines))
+    read_lines = lineno_read_lines(str(target))
+    unread = _unread_lines_in_range(read_lines, start_line, end_line, len(lines))
     if unread:
         preview = unread[:_UNREAD_PREVIEW]
         head = ", ".join(str(i) for i in preview)
         if len(unread) > _UNREAD_PREVIEW:
             head += f", … ({len(unread)} total)"
-        return f"error: lines {head} not read; call read_file(path, with_lineno=true) first to see current line numbers"
+        window = ""
+        if read_lines:
+            window = f" (this turn read lines {min(read_lines)}-{max(read_lines)})"
+        return (
+            f"error: lines {head} not read{window}; call read_file(path, with_lineno=true) "
+            "first — read with a small margin around the lines you plan to edit"
+        )
+
+    recorded_mtime = lineno_read_mtime(str(target))
+    if recorded_mtime is not None:
+        try:
+            current_mtime = target.stat().st_mtime_ns
+        except OSError:
+            current_mtime = None
+        if current_mtime is not None and current_mtime != recorded_mtime:
+            return (
+                f"error: {path} changed since it was read (line numbers may be stale); "
+                "re-read with read_file(path, with_lineno=true)"
+            )
 
     if start_line == len(lines) + 1:
         result = _append_after(target, path, text, lines, new_content)
     else:
         result = _replace_range(target, path, lines, start_line, end_line, new_content)
-    # Line numbers are stale after a write; force a re-read before next edit.
-    invalidate_lineno_read(str(target))
+    # Line numbers are stale after a write; the fresh mtime makes the next
+    # edit_lineno reject until the file is re-read.
     return result

src/plyngent/tools/file/edit_replace.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
-from plyngent.agent import ToolTag, invalidate_lineno_read, tool
-from plyngent.tools.workspace import resolve_path
+from plyngent.agent import ToolTag, tool
+from plyngent.tools.workspace import AccessMode, resolve_path
 
 
 def _count_non_overlapping(text: str, needle: str) -> int:
@@ -18,15 +18,31 @@ def _count_non_overlapping(text: str, needle: str) -> int:
         start = index + len(needle)
 
 
-def _success_message(path: str, *, replaced: int, found: int) -> str:
+def _excerpt(text: str, limit: int = 40) -> str:
+    """Collapse newlines and truncate for a one-line message excerpt."""
+    one = text.replace("\r\n", " ").replace("\n", " ")
+    if len(one) > limit:
+        return one[:limit] + "…"
+    return one
+
+
+def _success_message(
+    path: str,
+    *,
+    replaced: int,
+    found: int,
+    old_string: str,
+    new_string: str,
+) -> str:
     remaining = found - replaced
     unit = "occurrence" if replaced == 1 else "occurrences"
+    change = f" ('{_excerpt(old_string)}' → '{_excerpt(new_string)}')"
     if remaining == 0:
         if found == 1:
-            return f"replaced 1 occurrence in {path}"
-        return f"replaced {replaced} {unit} in {path} (all {found} matches)"
+            return f"replaced 1 occurrence in {path}{change}"
+        return f"replaced {replaced} {unit} in {path}{change} (all {found} matches)"
     return (
-        f"replaced {replaced} {unit} in {path} "
+        f"replaced {replaced} {unit} in {path}{change} "
         f"({replaced} of {found} matches; {remaining} remain — "
         f"raise max_replaces or use a more specific old_string)"
     )
@@ -44,7 +60,7 @@ async def edit_replace(path: str, old_string: str, new_string: str, max_replaces
         return "error: old_string must not be empty"
     if max_replaces < 1:
         return "error: max_replaces must be >= 1"
-    target = resolve_path(path)
+    target = resolve_path(path, required=AccessMode.WRITE)
     if not target.is_file():
         return f"error: not a file: {path}"
     text = target.read_text(encoding="utf-8", errors="replace")
@@ -54,6 +70,12 @@ async def edit_replace(path: str, old_string: str, new_string: str, max_replaces
     n = min(max_replaces, found)
     updated = text.replace(old_string, new_string, n)
     _ = target.write_text(updated, encoding="utf-8")
-    # Any lineno read state is stale after a write; force a re-read.
-    invalidate_lineno_read(str(target))
-    return _success_message(path, replaced=n, found=found)
+    # The write changes the file's mtime, so edit_lineno's freshness check
+    # rejects stale line numbers until the model re-reads with_lineno.
+    return _success_message(
+        path,
+        replaced=n,
+        found=found,
+        old_string=old_string,
+        new_string=new_string,
+    )

src/plyngent/tools/file/fs_ops.py

@@ -4,7 +4,7 @@ import shutil
 from pathlib import Path
 
 from plyngent.agent import ToolTag, invalidate_lineno_read, tool
-from plyngent.tools.workspace import WorkspaceError, get_workspace_root, resolve_path
+from plyngent.tools.workspace import AccessMode, WorkspaceError, get_workspace_root, resolve_path
 
 
 def _kind(path: Path) -> str:
@@ -26,18 +26,28 @@ def _remove_existing(path: Path) -> None:
 
 def _resolve_pair(src: str, dst: str) -> tuple[Path, Path, Path] | str:
     try:
-        source = resolve_path(src)
-        dest = resolve_path(dst)
+        source = resolve_path(src, required=AccessMode.READ)
+        dest = resolve_path(dst, required=AccessMode.WRITE)
         root = get_workspace_root()
     except WorkspaceError as exc:
         return f"error: {exc}"
     return source, dest, root
 
 
-def _prepare_dest(source: Path, dest: Path, root: Path, *, overwrite: bool, dst_label: str) -> Path | str:
+def _display(path: Path, root: Path) -> str:
+    """Workspace-relative display path, falling back to absolute outside the root."""
+    try:
+        return str(path.relative_to(root))
+    except ValueError:
+        return str(path)
+
+
+def _prepare_dest(source: Path, dest: Path, *, overwrite: bool, dst_label: str) -> Path | str:
     """Resolve copy/move destination; return error string on conflict."""
     if source.is_file() and dest.is_dir():
-        dest = resolve_path(str((dest / source.name).relative_to(root)))
+        # ``dest`` may be outside the primary root (temp workspace / grant), so
+        # resolve the child directly instead of relativizing against the root.
+        dest = resolve_path(str(dest / source.name), required=AccessMode.WRITE)
     if dest.exists() or dest.is_symlink():
         if not overwrite:
             return f"error: destination exists: {dst_label} (set overwrite=true)"
@@ -56,7 +66,7 @@ def _copy_or_move_validated(
     overwrite: bool,
     action: str,
 ) -> str:
-    prepared = _prepare_dest(source, dest, root, overwrite=overwrite, dst_label=dst)
+    prepared = _prepare_dest(source, dest, overwrite=overwrite, dst_label=dst)
     if isinstance(prepared, str):
         return prepared
     dest = prepared
@@ -68,13 +78,16 @@ def _copy_or_move_validated(
             else:
                 _ = shutil.copy2(source, dest, follow_symlinks=False)
                 label = _kind(source)
-            # A copy does not change the source, but the destination content is new.
+            # A copy does not change the source, but the destination content is
+            # new. copy2/copytree preserve the source mtime, so the freshness
+            # check alone could miss the change — invalidate explicitly.
             invalidate_lineno_read(str(dest))
-            return f"copied {label} {src} -> {dest.relative_to(root)}"
+            return f"copied {label} {src} -> {_display(dest, root)}"
         moved = Path(shutil.move(str(source), str(dest))).resolve()
+        # shutil.move preserves mtime too; drop read state for both paths.
         invalidate_lineno_read(str(source))
         invalidate_lineno_read(str(moved))
-        return f"moved {_kind(moved)} {src} -> {moved.relative_to(root)}"
+        return f"moved {_kind(moved)} {src} -> {_display(moved, root)}"
     except WorkspaceError as exc:
         return f"error: {exc}"
     except OSError as exc:
@@ -144,7 +157,7 @@ async def delete_path(path: str, *, recursive: bool = False) -> str:
     ``recursive=true`` (uses ``shutil.rmtree``). The workspace root cannot be deleted.
     """
     try:
-        target = resolve_path(path)
+        target = resolve_path(path, required=AccessMode.WRITE)
         root = get_workspace_root()
     except WorkspaceError as exc:
         return f"error: {exc}"

src/plyngent/tools/file/get_truncated.py

@@ -6,26 +6,68 @@ from typing import cast
 
 from plyngent.agent import ToolTag, tool
 from plyngent.agent.budget import DEFAULT_TOOL_RESULT_MAX_CHARS
-from plyngent.tools.file.read import line_range_label, read_raw_text
+from plyngent.tools.file.read import line_range_label, read_file, read_raw_text
 from plyngent.tools.net.fetch import fetch
 from plyngent.tools.truncate_token import (
+    TruncateToken,
     decode_truncate_token,
     get_remainder,
     truncate_with_token,
 )
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+def _memory_chunk(parsed: TruncateToken, max_chars: int) -> str:
+    """Serve one chunk from the in-memory remainder store (or an error)."""
+    remainder = get_remainder(parsed.location)
+    if remainder is None:
+        return "error: truncate token expired (no longer in memory); re-run the tool"
+    start = parsed.offset
+    segment = remainder[start : start + max_chars]
+    chunk, _ = truncate_with_token(
+        segment,
+        max_chars,
+        kind="memory",
+        location=parsed.location,
+        offset=start,
+        limit=max_chars,
+        total_len=len(remainder),
+    )
+    return chunk
+
+
+async def _numbered_continuation(text: str, location: str, char_offset: int, max_chars: int) -> str:
+    """Resume a numbered read at the line containing *char_offset*.
+
+    Delegates to ``read_file(with_lineno=True)`` so the continuation carries
+    ``N|`` line numbers and marks the resumed lines readable for ``edit_lineno``.
+    """
+    pos = 0
+    line = 0
+    for ln in text.splitlines(keepends=True):
+        if pos + len(ln) > char_offset:
+            break
+        pos += len(ln)
+        line += 1
+    return await read_file.handler(
+        location,
+        offset=line,
+        with_lineno=True,
+        max_chars=max_chars,
+    )
+
+
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def get_truncated(token: str, *, max_chars: int = DEFAULT_TOOL_RESULT_MAX_CHARS) -> str:
     """Fetch the next chunk of a truncated result using its ``truncate_token``.
 
     Pass the token shown at the end of a truncated ``read_file``, ``fetch``,
     ``run_command``, or earlier ``get_truncated`` result to keep reading without
     re-requesting the whole source or raising limits. Truncated output carries a
-    fresh token, so chunks chain indefinitely. File chunks start with a 1-based
-    ``L{begin}-{end}`` line range like ``read_file``; memory chunks (generic
-    tool output) are served from a short-lived in-memory store that is forgotten
-    when the agent exits.
+    fresh token, so chunks chain indefinitely. File chunks resume in the same
+    view as the original read: numbered reads continue as numbered lines
+    (editable via ``edit_lineno``), plain reads as raw text with a 1-based
+    ``L{begin}-{end}`` range. Memory chunks (generic tool output) are served
+    from a short-lived in-memory store that is forgotten when the agent exits.
     """
     parsed = decode_truncate_token(token)
     if parsed is None:
@@ -33,26 +75,14 @@ async def get_truncated(token: str, *, max_chars: int = DEFAULT_TOOL_RESULT_MAX_
     if parsed.kind == "http":
         return await fetch.handler(parsed.location, offset=parsed.offset, max_chars=parsed.limit)
     if parsed.kind == "memory":
-        remainder = get_remainder(parsed.location)
-        if remainder is None:
-            return "error: truncate token expired (no longer in memory); re-run the tool"
-        start = parsed.offset
-        segment = remainder[start : start + max_chars]
-        chunk, _ = truncate_with_token(
-            segment,
-            max_chars,
-            kind="memory",
-            location=parsed.location,
-            offset=start,
-            limit=max_chars,
-            total_len=len(remainder),
-        )
-        return chunk
+        return _memory_chunk(parsed, max_chars)
     text, err = read_raw_text(parsed.location)
     if err:
         return err
     text = cast("str", text)
     start = parsed.offset
+    if parsed.numbered:
+        return await _numbered_continuation(text, parsed.location, start, max_chars)
     segment = text[start : start + max_chars]
     chunk, _ = truncate_with_token(
         segment,

src/plyngent/tools/file/glob_paths.py

@@ -4,7 +4,7 @@ from typing import TYPE_CHECKING
 
 from plyngent.agent import ToolTag, tool
 from plyngent.tools.file.tree import VCS_DIR_NAMES
-from plyngent.tools.workspace import WorkspaceError, get_workspace_root, resolve_path
+from plyngent.tools.workspace import AccessMode, WorkspaceError, get_workspace_root, resolve_path
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -57,7 +57,7 @@ def _collect_glob(
 def _resolve_glob_base(path: str) -> tuple[Path, Path] | str:
     try:
         root = get_workspace_root()
-        base = resolve_path(path)
+        base = resolve_path(path, required=AccessMode.READ)
     except WorkspaceError as exc:
         return f"error: {exc}"
     if not base.is_dir():
@@ -65,7 +65,7 @@ def _resolve_glob_base(path: str) -> tuple[Path, Path] | str:
     return root, base
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def glob_paths(
     pattern: str,
     path: str = ".",

src/plyngent/tools/file/grep_files.py

@@ -5,7 +5,7 @@ from typing import TYPE_CHECKING
 
 from plyngent.agent import ToolTag, tool
 from plyngent.tools.file.tree import VCS_DIR_NAMES
-from plyngent.tools.workspace import WorkspaceError, get_workspace_root, resolve_path
+from plyngent.tools.workspace import AccessMode, WorkspaceError, get_workspace_root, resolve_path
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
@@ -65,7 +65,7 @@ def _iter_files(base: Path, *, skip_hidden_dirs: bool) -> list[Path]:
 
 def _resolve_files(path: str, *, skip_hidden_dirs: bool) -> list[Path] | str:
     try:
-        base = resolve_path(path)
+        base = resolve_path(path, required=AccessMode.READ)
     except WorkspaceError as exc:
         return f"error: {exc}"
     if not base.exists():
@@ -127,7 +127,7 @@ def _compile_pattern(pattern: str, *, case_insensitive: bool) -> re.Pattern[str]
         return f"error: invalid regex: {exc}"
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def grep_files(
     pattern: str,
     path: str = ".",

src/plyngent/tools/file/listdir.py

@@ -1,13 +1,13 @@
 from __future__ import annotations
 
 from plyngent.agent import ToolTag, tool
-from plyngent.tools.workspace import resolve_path
+from plyngent.tools.workspace import AccessMode, resolve_path
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def listdir(path: str = ".") -> str:
     """List entries in a directory under the workspace (name and type)."""
-    target = resolve_path(path)
+    target = resolve_path(path, required=AccessMode.READ)
     if not target.is_dir():
         return f"error: not a directory: {path}"
     lines: list[str] = []

src/plyngent/tools/file/read.py

@@ -4,8 +4,8 @@ from typing import cast
 
 from plyngent.agent import ToolTag, mark_lineno_read, tool
 from plyngent.agent.budget import DEFAULT_TOOL_RESULT_MAX_CHARS
-from plyngent.tools.truncate_token import truncate_with_token
-from plyngent.tools.workspace import resolve_path
+from plyngent.tools.truncate_token import TruncateToken, truncate_with_token, truncation_marker
+from plyngent.tools.workspace import AccessMode, resolve_path
 
 _LINENO_WIDTH = 6
 
@@ -41,7 +41,7 @@ def read_raw_text(path: str) -> tuple[str | None, str]:
     always refer to the raw file text (never the ``L{begin}-{end}`` header).
     Missing paths and directories are distinguished for the caller.
     """
-    target = resolve_path(path)
+    target = resolve_path(path, required=AccessMode.READ)
     if not target.exists():
         return None, f"error: file not found: {path}"
     if not target.is_file():
@@ -49,7 +49,7 @@ def read_raw_text(path: str) -> tuple[str | None, str]:
     return target.read_text(encoding="utf-8", errors="replace"), ""
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def read_file(
     path: str,
     *,
@@ -64,13 +64,15 @@ async def read_file(
     (None = rest of file). When ``with_lineno`` is true, each line is prefixed
     with its 1-based file line number (``     N|…``), matching ``edit_lineno``
     numbering, and those lines are marked readable for ``edit_lineno`` this turn.
+    Only the displayed lines become editable, so read with a small margin around
+    any range you plan to edit with ``edit_lineno``.
 
     ``max_chars`` caps the returned slice (default: the agent's tool-result cap,
     ``DEFAULT_TOOL_RESULT_MAX_CHARS``); a ``truncate_token`` is appended when cut
     so ``get_truncated`` can continue reading the rest without a new request.
     Pass ``max_chars < 1`` to read unbounded.
     """
-    target = resolve_path(path)
+    target = resolve_path(path, required=AccessMode.READ)
     text, err = read_raw_text(path)
     if err:
         return err
@@ -83,14 +85,10 @@ async def read_file(
     if start >= len(lines):
         return ""
     slice_lines = lines[start:end]
-    if with_lineno:
-        mark_lineno_read(str(target), set(range(start + 1, end + 1)))
-        body = _format_with_lineno(slice_lines, start_lineno=start + 1)
-    else:
-        body = "".join(slice_lines)
+    body = _format_with_lineno(slice_lines, start_lineno=start + 1) if with_lineno else "".join(slice_lines)
+    char_start = len("".join(lines[:start]))
     if max_chars >= 1:
-        char_start = len("".join(lines[:start]))
-        body, _ = truncate_with_token(
+        body, token = truncate_with_token(
             body,
             max_chars,
             kind="file",
@@ -102,10 +100,39 @@ async def read_file(
             # returned slice itself was cut by max_chars (not just "file continues").
             emit_more_after=False,
         )
+    else:
+        token = None
     if not body:
         return ""
     if with_lineno:
-        return body  # per-line numbers already show the range
+        # Mark only the lines actually displayed: complete numbered lines in the
+        # returned body (the [Truncated] marker, when present, is not a file line).
+        # The max_chars-truncated tail was never shown, so it stays unread —
+        # edit_lineno must not trust line numbers the model never saw.
+        counted = body
+        if token is not None:
+            counted = body.split("\n[Truncated", 1)[0]
+            shown = counted.count("\n")
+            # The truncate cursor counts *numbered* chars (each line carries an
+            # "N|" prefix), which would over-advance into raw text and skip
+            # lines on continuation. Rebase the token onto raw characters of the
+            # complete lines shown (at least one, so the cursor always moves)
+            # and mark it as the numbered view for get_truncated.
+            consumed_lines = max(shown, 1)
+            raw_consumed = sum(len(ln) for ln in slice_lines[:consumed_lines])
+            corrected = TruncateToken(
+                kind="file",
+                location=path,
+                offset=char_start + raw_consumed,
+                limit=max_chars,
+                numbered=True,
+            )
+            omitted = len(text) - (char_start + raw_consumed)
+            body = counted + truncation_marker(max_chars, omitted, corrected)
+        else:
+            shown = counted.count("\n")
+        mark_lineno_read(str(target), set(range(start + 1, start + 1 + shown)))
+        return body
     begin = start + 1
     end_line = start + len(slice_lines)
     return f"L{begin}-{end_line}\n{body}"

src/plyngent/tools/file/tree.py

@@ -1,15 +1,20 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Literal
 
 from plyngent.agent import ToolTag, tool
-from plyngent.tools.workspace import WorkspaceError, get_path_denylist, resolve_path
+from plyngent.tools.workspace import AccessMode, WorkspaceError, get_path_denylist, resolve_path
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from pathlib import Path
 
+# Model-facing renderings. ``markdown`` (default) is the cheapest, most
+# reliable representation for the agent; ``flat`` gives directly-usable paths;
+# ``decorated`` keeps the classic box-drawing tree for human readers.
+type TreeFormat = Literal["markdown", "flat", "decorated"]
+
 DEFAULT_MAX_DEPTH = 4
 DEFAULT_MAX_ENTRIES = 50
 
@@ -144,6 +149,80 @@ def _render_tree(
         lines.append(f"{prefix}└── … ({more} more entries not shown)")
 
 
+def _render_tree_markdown(
+    directory: Path,
+    *,
+    prefix: str,
+    depth: int,
+    limits: _TreeLimits,
+    lines: list[str],
+) -> None:
+    """Nested ``- `` bullet list (2-space indent per level)."""
+    if depth >= limits.max_depth:
+        return
+
+    children = _list_children(directory, limits=limits)
+    if isinstance(children, str):
+        lines.append(f"{prefix}- {children}")
+        return
+
+    truncated = len(children) > limits.max_entries
+    shown = children[: limits.max_entries]
+    for child in shown:
+        try:
+            is_dir = child.is_dir()
+        except OSError:
+            lines.append(f"{prefix}- {child.name} [error: stat failed]")
+            continue
+        if is_dir:
+            lines.append(f"{prefix}- {child.name}/")
+            _render_tree_markdown(
+                child,
+                prefix=prefix + "  ",
+                depth=depth + 1,
+                limits=limits,
+                lines=lines,
+            )
+        else:
+            lines.append(f"{prefix}- {child.name}")
+
+    if truncated:
+        more = len(children) - limits.max_entries
+        lines.append(f"{prefix}- … ({more} more entries not shown)")
+
+
+def _flat_paths(directory: Path, *, limits: _TreeLimits) -> list[str]:
+    """All paths (dirs with trailing ``/``, files plain) in depth-first order.
+
+    Includes empty directories; bounded by *max_depth* (``max_entries`` is
+    applied to the total by the caller).
+    """
+    out: list[str] = []
+
+    def visit(child_dir: Path, rel: str, depth: int) -> None:
+        if depth >= limits.max_depth:
+            return
+        children = _list_children(child_dir, limits=limits)
+        if isinstance(children, str):
+            out.append(f"{rel or child_dir.name} [error: cannot list]")
+            return
+        for child in children:
+            try:
+                is_dir = child.is_dir()
+            except OSError:
+                out.append(f"{child.name} [error: stat failed]")
+                continue
+            child_rel = child.name if not rel else f"{rel}/{child.name}"
+            if is_dir:
+                out.append(f"{child_rel}/")
+                visit(child, child_rel, depth + 1)
+            else:
+                out.append(child_rel)
+
+    visit(directory, "", 0)
+    return out
+
+
 def _resolve_skip_basenames(skip_dirs: Sequence[str] | None) -> frozenset[str]:
     """None → default noise set; explicit list (including empty) replaces defaults."""
     if skip_dirs is None:
@@ -151,10 +230,11 @@ def _resolve_skip_basenames(skip_dirs: Sequence[str] | None) -> frozenset[str]:
     return frozenset(name for name in skip_dirs if name)
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def tree(
     path: str = ".",
     *,
+    format: TreeFormat = "markdown",  # noqa: A002 — model-facing param name
     max_depth: int = DEFAULT_MAX_DEPTH,
     max_entries: int = DEFAULT_MAX_ENTRIES,
     skip_hidden_dirs: bool = True,
@@ -174,8 +254,15 @@ async def tree(
     ``apply_path_denylist`` (default true) hides entries whose full path matches
     the agent ``path_denylist`` policy.
 
+    ``format`` selects the representation (the model chooses per call):
+    ``markdown`` (default) renders a nested ``- `` bullet list — cheapest and
+    most reliable for the agent; ``flat`` lists one relative path per line
+    (directories with a trailing ``/``) so every path is directly usable
+    without reconstructing it; ``decorated`` uses the classic box-drawing tree.
+
     ``max_depth`` limits how deep directories are expanded (1 = origin + children).
-    ``max_entries`` caps how many entries are listed per directory.
+    ``max_entries`` caps entries per directory (``markdown``/``decorated``) or
+    the total number of lines (``flat``).
     """
     if max_depth < 1:
         return "error: max_depth must be >= 1"
@@ -183,14 +270,12 @@ async def tree(
         return "error: max_entries must be >= 1"
 
     try:
-        origin = resolve_path(path)
+        origin = resolve_path(path, required=AccessMode.READ)
     except WorkspaceError as exc:
         return f"error: {exc}"
     if not origin.is_dir():
         return f"error: not a directory: {path}"
 
-    root_label = path.rstrip("/\\") or "."
-    lines = [f"{root_label}/"]
     limits = _TreeLimits(
         max_depth=max_depth,
         max_entries=max_entries,
@@ -198,7 +283,18 @@ async def tree(
         skip_basenames=_resolve_skip_basenames(skip_dirs),
         apply_path_denylist=apply_path_denylist,
     )
-    _render_tree(
+
+    if format == "flat":
+        paths = _flat_paths(origin, limits=limits)
+        lines = paths[:max_entries]
+        if len(paths) > max_entries:
+            lines.append(f"… ({len(paths) - max_entries} more paths not shown)")
+        return "\n".join(lines)
+
+    root_label = path.rstrip("/\\") or "."
+    lines: list[str] = [] if format == "markdown" else [f"{root_label}/"]
+    renderer = _render_tree_markdown if format == "markdown" else _render_tree
+    renderer(
         origin,
         prefix="",
         depth=0,

src/plyngent/tools/file/write.py

@@ -1,14 +1,15 @@
 from __future__ import annotations
 
-from plyngent.agent import ToolTag, invalidate_lineno_read, tool
-from plyngent.tools.workspace import resolve_path
+from plyngent.agent import ToolTag, tool
+from plyngent.tools.workspace import AccessMode, resolve_path
 
 
 @tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.YOLO)
 async def write_file(path: str, content: str) -> str:
     """Write text content to a file under the workspace (creates parents)."""
-    target = resolve_path(path)
+    target = resolve_path(path, required=AccessMode.WRITE)
     target.parent.mkdir(parents=True, exist_ok=True)
     _ = target.write_text(content, encoding="utf-8")
-    invalidate_lineno_read(str(target))
+    # The write changes the file's mtime, so edit_lineno's freshness check
+    # rejects stale line numbers until the model re-reads with_lineno.
     return f"wrote {len(content)} characters to {path}"

src/plyngent/tools/mcp.py

@@ -0,0 +1,108 @@
+"""Register MCP server tools into the tool catalog (namespaced, LOCAL tags).
+
+Mirrors :mod:`plyngent.tools.plugins`: the catalog only *registers* what the
+model may see; hosts still select into a :class:`ToolRegistry`. Connections
+must already be started (see :class:`~plyngent.runtime.mcp_client.McpManager`);
+this module is sync-only so registry rebuilds never need an event loop.
+
+Tool names are namespaced ``mcp__<server>__<tool>`` so two servers (or a
+server and a builtin) can never collide on sanitized names; the catalog still
+refuses true clashes.
+"""
+
+from __future__ import annotations
+
+import re
+from typing import TYPE_CHECKING
+
+from plyngent.agent.tools import ToolDefinition, ToolTag
+from plyngent.tools.catalog import ToolSource, get_catalog
+
+if TYPE_CHECKING:
+    from collections.abc import Awaitable, Callable
+
+    from plyngent.config.models import McpConfig
+    from plyngent.runtime.mcp_client import McpManager, McpTool
+
+_MCP_PREFIX = "mcp__"
+_NAME_SEGMENT_MAX = 64
+_SANITIZE_PATTERN = re.compile(r"[^A-Za-z0-9_-]")
+
+
+def _sanitize_segment(part: str) -> str:
+    """Reduce a server/tool name to a model-safe, bounded name segment."""
+    return _SANITIZE_PATTERN.sub("_", part)[:_NAME_SEGMENT_MAX] or "srv"
+
+
+def mcp_tool_name(server: str, tool: str) -> str:
+    """Namespaced catalog name for one MCP tool (collision-free per server)."""
+    return f"{_MCP_PREFIX}{_sanitize_segment(server)}__{_sanitize_segment(tool)}"
+
+
+def _make_handler(
+    manager: McpManager,
+    server: str,
+    tool: str,
+) -> Callable[..., Awaitable[str]]:
+    async def handler(**arguments: object) -> str:
+        return await manager.call(server, tool, dict(arguments))
+
+    return handler
+
+
+def register_mcp_server_tools(
+    server: str,
+    tools: list[McpTool],
+    *,
+    manager: McpManager,
+    read_only: bool = False,
+) -> list[str]:
+    """Register one server's advertised tools; returns the registered names.
+
+    Tags: LOCAL (plus READ_ONLY when the server config opts in) — never YOLO or
+    TRUSTABLE, so host-side danger classification always sees every call.
+    """
+    catalog = get_catalog()
+    source = ToolSource(kind="mcp", plugin_id=server)
+    names: list[str] = []
+    for entry in tools:
+        if not entry.name:
+            continue
+        tags = ToolTag.LOCAL
+        if read_only:
+            tags |= ToolTag.READ_ONLY
+        description = entry.description or f"MCP tool {entry.name!r} from server {server!r}"
+        definition = ToolDefinition(
+            name=mcp_tool_name(server, entry.name),
+            description=f"[mcp:{server}] {description}",
+            parameters=dict(entry.input_schema),
+            handler=_make_handler(manager, server, entry.name),
+            tags=tags,
+        )
+        catalog.register(definition, source=source)
+        names.append(definition.name)
+    return names
+
+
+def purge_mcp_tools() -> int:
+    """Remove previously registered MCP tools (call before re-registering)."""
+    return get_catalog().purge_kind("mcp")
+
+
+def register_mcp_tools(manager: McpManager, config: McpConfig) -> list[str]:
+    """Register every connected server's tools; replaces prior MCP entries."""
+    _ = purge_mcp_tools()
+    names: list[str] = []
+    for connection in manager.connections():
+        if not connection.connected or not connection.tools:
+            continue
+        server_cfg = config.servers.get(connection.name)
+        names.extend(
+            register_mcp_server_tools(
+                connection.name,
+                connection.tools,
+                manager=manager,
+                read_only=server_cfg.read_only if server_cfg is not None else False,
+            )
+        )
+    return names

src/plyngent/tools/net/fetch.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 from plyngent.agent import ToolTag, tool
+from plyngent.tools.context import is_read_only_context
 from plyngent.tools.net.client import http_fetch
 from plyngent.tools.net.policy import (
     DEFAULT_MAX_BODY_CHARS_IN,
@@ -66,7 +67,7 @@ def format_fetch_result(
     return "\n".join(parts)
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.YOLO | ToolTag.TRUSTABLE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.YOLO | ToolTag.TRUSTABLE | ToolTag.READ_ONLY)
 async def fetch(
     url: str,
     *,
@@ -92,9 +93,13 @@ async def fetch(
     Private/loopback/link-local hosts require an explicit human policy grant
     (not skipped by YOLO). HTTPS→HTTP redirects are blocked unless
     ``allow_http_downgrade`` is true.
+
+    Read-only contexts (e.g. ``/btw --tools=read``) accept only ``GET``.
     """
     try:
         verb = normalize_method(method)
+        if is_read_only_context() and verb != "GET":
+            return "error: fetch method must be GET in a read-only context (POST/PUT/DELETE mutate)"
         parsed = parse_fetch_url(url)
         hdrs = normalize_request_headers(headers, user_agent=user_agent)
         body_bytes: bytes | None = None

src/plyngent/tools/process/command_exec.py

@@ -10,6 +10,7 @@ if TYPE_CHECKING:
     from pathlib import Path
 
 from plyngent.tools.workspace import (
+    AccessMode,
     WorkspaceError,
     check_command_allowed,
     get_workspace_root,
@@ -61,7 +62,7 @@ def format_command_result(
 
 def resolve_workdir(cwd: str) -> tuple["Path", str]:
     """Return (absolute workdir, display path relative to workspace when possible)."""
-    workdir = resolve_path(cwd)
+    workdir = resolve_path(cwd, required=AccessMode.EXEC)
     if not workdir.is_dir():
         msg = f"not a directory: {cwd}"
         raise WorkspaceError(msg)

src/plyngent/tools/process/pty_session.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, ClassVar, cast
 
 from plyngent.tools.process.pty_backend import PtyHandle, pty_available, spawn_pty
 from plyngent.tools.process.pty_terminal import sanitize_pty_output_for_tool
-from plyngent.tools.workspace import WorkspaceError, check_command_allowed, resolve_path
+from plyngent.tools.workspace import AccessMode, WorkspaceError, check_command_allowed, resolve_path
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -122,7 +122,7 @@ class PtyManager:
             msg = "PTY is not available on this platform (Windows needs pywinpty)"
             raise WorkspaceError(msg)
         check_command_allowed(command)
-        workdir = resolve_path(cwd)
+        workdir = resolve_path(cwd, required=AccessMode.EXEC)
         if not workdir.is_dir():
             msg = f"cwd is not a directory: {cwd}"
             raise WorkspaceError(msg)

src/plyngent/tools/todo.py

@@ -48,7 +48,7 @@ async def _with_todo_stack(mutator: Callable[[TodoStack], str]) -> str:
     return result
 
 
-@tool(name="todo_list", tags=ToolTag.LOCAL | ToolTag.PUBLIC | ToolTag.SESSION_STATE)
+@tool(name="todo_list", tags=ToolTag.LOCAL | ToolTag.PUBLIC | ToolTag.SESSION_STATE | ToolTag.READ_ONLY)
 async def todo_list() -> str:
     """Show the LIFO stack of **task groups** (TOP group = current breakdown level).
 

src/plyngent/tools/truncate_token.py

@@ -37,13 +37,15 @@ class TruncateToken(msgspec.Struct, frozen=True):
     lines (files is line-based via ``read_file``); ``get_truncated`` interprets
     by ``kind``. For ``memory``, ``location`` is a key into the in-memory
     remainder store and ``offset``/``limit`` index characters of that stored
-    remainder.
+    remainder. ``numbered`` marks file tokens from ``read_file(with_lineno)``:
+    the continuation resumes the numbered view instead of raw text.
     """
 
     kind: TruncateKind
     location: str
     offset: int
     limit: int
+    numbered: bool = False
 
 
 # In-memory remainders for generic (non-resumable) tool output. Process-lifetime

src/plyngent/tools/vcs/tools.py

@@ -22,7 +22,7 @@ def _backend_or_error() -> VcsBackend | str:
     return backend
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def vcs_kind() -> str:
     """Return the detected VCS kind under the workspace (e.g. ``git``), or an error."""
     backend = _backend_or_error()
@@ -31,7 +31,7 @@ async def vcs_kind() -> str:
     return backend.kind
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def vcs_status() -> str:
     """Show working-tree status for the detected VCS (read-only)."""
     backend = _backend_or_error()
@@ -40,7 +40,7 @@ async def vcs_status() -> str:
     return backend.status()
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def vcs_diff(path: str = "", *, staged: bool = False) -> str:
     """Show a unified diff for the detected VCS (read-only).
 
@@ -54,7 +54,7 @@ async def vcs_diff(path: str = "", *, staged: bool = False) -> str:
     return backend.diff(staged=staged, path=rel)
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def vcs_log(limit: int = 10) -> str:
     """Show recent commits for the detected VCS (read-only)."""
     if limit < 1:
@@ -65,7 +65,7 @@ async def vcs_log(limit: int = 10) -> str:
     return backend.log(limit=limit)
 
 
-@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE)
+@tool(tags=ToolTag.LOCAL | ToolTag.INSTANCE_STATE | ToolTag.READ_ONLY)
 async def vcs_branch() -> str:
     """Show the current branch / named head for the detected VCS (read-only)."""
     backend = _backend_or_error()

src/plyngent/tools/workspace.py

@@ -1,13 +1,14 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
+from enum import IntEnum
 from pathlib import Path
 from typing import TYPE_CHECKING, cast
 
 if TYPE_CHECKING:
-    from collections.abc import Callable, Sequence
+    from collections.abc import Callable, Mapping, Sequence
 
-    from plyngent.tools.context import InstanceState
+    from plyngent.tools.context import InstanceState, SessionState
 
 DEFAULT_COMMAND_DENYLIST: frozenset[str] = frozenset(
     {
@@ -39,6 +40,36 @@ MAX_TEMPORARY_WORKSPACES = 16
 # Timed human override for command denylist (independent of YOLO soft-confirm).
 DEFAULT_POLICY_CONFIRM_TIMEOUT_SECONDS = 30.0
 
+
+class AccessMode(IntEnum):
+    """Ordered access level for path grants outside the workspace root.
+
+    A grant satisfies a requirement when its value is ``>=`` the requirement
+    (``read`` < ``write`` < ``exec``); ``exec`` also implies file writes.
+    """
+
+    READ = 1
+    WRITE = 2
+    EXEC = 3
+
+
+_ACCESS_MODE_NAMES: dict[str, AccessMode] = {
+    "read": AccessMode.READ,
+    "write": AccessMode.WRITE,
+    "exec": AccessMode.EXEC,
+}
+
+
+def parse_access_mode(value: str) -> AccessMode | None:
+    """Parse a case-insensitive mode token (``read`` / ``write`` / ``exec``)."""
+    return _ACCESS_MODE_NAMES.get(value.strip().lower())
+
+
+def mode_covers(granted: AccessMode, required: AccessMode) -> bool:
+    """Whether a grant at *granted* satisfies a tool that needs *required*."""
+    return granted >= required
+
+
 # Hook: (basename, argv, timeout_seconds) -> True allow for this session basename.
 type PolicyConfirmHook = Callable[[str, Sequence[str], float], bool]
 
@@ -63,6 +94,10 @@ class WorkspacePolicy:
     policy_allowed_commands: set[str] = field(default_factory=set)
     policy_confirm_hook: PolicyConfirmHook | None = None
     policy_confirm_timeout_seconds: float = DEFAULT_POLICY_CONFIRM_TIMEOUT_SECONDS
+    # Static TOML pre-allow (resolved path → mode); never prompts.
+    config_allow: dict[Path, AccessMode] = field(default_factory=dict)
+    # Process-scoped YOLO / --yes grants (resolved path → mode); never persisted.
+    yolo_allow: dict[Path, AccessMode] = field(default_factory=dict)
 
 
 def _bound_instance() -> InstanceState | None:
@@ -71,6 +106,12 @@ def _bound_instance() -> InstanceState | None:
     return get_instance()
 
 
+def _bound_session() -> SessionState | None:
+    from plyngent.tools.context import get_session
+
+    return get_session()
+
+
 def require_bound_instance() -> InstanceState:
     """Return the bound instance or raise :class:`WorkspaceError`."""
     instance = _bound_instance()
@@ -243,11 +284,55 @@ def _under_any_root(resolved: Path, instance: InstanceState, policy: WorkspacePo
     return False
 
 
-def resolve_path(path: str | Path) -> Path:
-    """Resolve ``path`` under the workspace root or an allowlisted temp root.
+def granted_access_mode(resolved: Path) -> AccessMode | None:
+    """Highest config / session / process mode covering *resolved*, if any."""
+    policy = active_workspace_policy()
+    session = _bound_session()
+    buckets: list[Mapping[Path, AccessMode]] = [policy.config_allow, policy.yolo_allow]
+    if session is not None:
+        buckets.append(session.access_grants)
+    best: AccessMode | None = None
+    for grants in buckets:
+        for root, granted in grants.items():
+            if (resolved == root or resolved.is_relative_to(root)) and (best is None or granted > best):
+                best = granted
+    return best
+
+
+def _path_grant_covers(resolved: Path, required: AccessMode) -> bool:
+    """Whether a config / session / process grant covers *resolved*."""
+    granted = granted_access_mode(resolved)
+    return granted is not None and mode_covers(granted, required)
+
+
+def within_workspace_roots(resolved: Path) -> bool:
+    """Whether *resolved* is under the primary root(s) or a temp allowlist root."""
+    instance = require_bound_instance()
+    return _under_any_root(resolved, instance, instance.workspace)
+
+
+def denylist_match(resolved: Path, *, directory: bool = False) -> str | None:
+    """Return the path denylist pattern matching *resolved*, or ``None``.
+
+    *directory* also matches a trailing-separator pattern (``/secret/``) against
+    the directory path itself, not just its children.
+    """
+    resolved_str = str(resolved).replace("\\", "/")
+    if directory and not resolved_str.endswith("/"):
+        resolved_str += "/"
+    for pattern in active_workspace_policy().path_denylist:
+        if pattern and pattern.replace("\\", "/") in resolved_str:
+            return pattern
+    return None
+
+
+def resolve_path(path: str | Path, *, required: AccessMode = AccessMode.WRITE) -> Path:
+    """Resolve ``path`` under the workspace root, an allowlist root, or a grant.
 
     Relative paths resolve against the **primary** workspace root. Absolute
-    paths may also land under a temporary workspace allowlist entry.
+    paths may also land under a temporary workspace allowlist entry or a
+    directory-access grant; ``required`` is the access mode the caller needs
+    (default :attr:`AccessMode.WRITE`, the conservative choice).
     """
     instance = require_bound_instance()
     policy = instance.workspace
@@ -256,15 +341,17 @@ def resolve_path(path: str | Path) -> Path:
     if not candidate.is_absolute():
         candidate = root / candidate
     resolved = candidate.expanduser().resolve()
-    if not _under_any_root(resolved, instance, policy):
-        msg = f"path escapes workspace root ({root}): {path}"
+    if not _under_any_root(resolved, instance, policy) and not _path_grant_covers(resolved, required):
+        msg = (
+            f"path escapes workspace root ({root}): {path}; "
+            "call request_directory_access to request access to a directory outside the workspace"
+        )
         raise WorkspaceError(msg)
     # Normalize separators so denylist entries like ``/secrets/`` match on Windows.
-    resolved_str = str(resolved).replace("\\", "/")
-    for pattern in policy.path_denylist:
-        if pattern and pattern.replace("\\", "/") in resolved_str:
-            msg = f"path denied by policy (matched {pattern!r}): {path}"
-            raise WorkspaceError(msg)
+    matched = denylist_match(resolved)
+    if matched is not None:
+        msg = f"path denied by policy (matched {matched!r}): {path}"
+        raise WorkspaceError(msg)
     return resolved
 
 

tests/test_agent/test_run_aside.py

@@ -209,3 +209,91 @@ async def test_run_aside_tools_clones_registry_with_fresh_session() -> None:
         pass
     assert hits == ["ok"]
     assert "aside" not in main_session.extras
+
+
+async def test_run_aside_read_only_clone_excludes_write_tools() -> None:
+    """A read-only-cloned registry passed to run_aside exposes no write tools."""
+    hits: list[str] = []
+
+    @tool(tags=ToolTag.LOCAL | ToolTag.READ_ONLY, register=False)
+    async def peek() -> str:
+        hits.append("peek")
+        return "peeked"
+
+    @tool(tags=ToolTag.LOCAL, register=False)
+    async def write_thing() -> str:
+        hits.append("write")
+        return "wrote"
+
+    registry = ToolRegistry([peek, write_thing], auto_bind_state=True)
+
+    def make_client(first_tool: str | None) -> Any:
+        calls = 0
+
+        class _Client:
+            @overload
+            async def chat_completions(
+                self, param: ChatCompletionsParam, *, stream: Literal[False] = False
+            ) -> ChatCompletionResponse: ...
+
+            @overload
+            async def chat_completions(
+                self, param: ChatCompletionsParam, *, stream: Literal[True]
+            ) -> AsyncIterator[ChatCompletionChunk]: ...
+
+            async def chat_completions(
+                self, param: ChatCompletionsParam, *, stream: bool = False
+            ) -> ChatCompletionResponse | AsyncIterator[ChatCompletionChunk]:
+                del stream, param
+                nonlocal calls
+                calls += 1
+                if calls == 1 and first_tool is not None:
+                    from plyngent.lmproto.openai_compatible.model import (
+                        AssistantFunctionTool,
+                        AssistantFunctionToolCall,
+                    )
+
+                    message = AssistantChatMessage(
+                        content="",
+                        tool_calls=[
+                            AssistantFunctionToolCall(
+                                id="c1",
+                                function=AssistantFunctionTool(name=first_tool, arguments="{}"),
+                            )
+                        ],
+                    )
+                    finish = "tool_calls"
+                else:
+                    message = AssistantChatMessage(content="done")
+                    finish = "stop"
+                return ChatCompletionResponse(
+                    id="1",
+                    object="chat.completion",
+                    created=0,
+                    model="m",
+                    choices=[
+                        ChatCompletionChoice(
+                            index=0,
+                            message=message,
+                            logprobs={},
+                            finish_reason=finish,
+                        )
+                    ],
+                    system_fingerprint="",
+                    usage={},
+                )
+
+        return _Client()
+
+    # Read-only tool is available to the side turn.
+    agent_peek = ChatAgent(make_client("peek"), model="m", tools=registry, stream=False)
+    async for _ in agent_peek.run_aside("go", tools=registry.clone(read_only_only=True)):
+        pass
+    assert hits == ["peek"]
+
+    # Write tool is not in the read-only clone: the call errors, never runs.
+    hits.clear()
+    agent_write = ChatAgent(make_client("write_thing"), model="m", tools=registry, stream=False)
+    async for _ in agent_write.run_aside("go", tools=registry.clone(read_only_only=True)):
+        pass
+    assert hits == []

tests/test_cli/test_display.py

@@ -65,7 +65,7 @@ async def test_flush_markdown_on_source_change(
 
     call = AssistantFunctionToolCall(
         id="1",
-        function=AssistantFunctionTool(name="run_argv", arguments='{"argv": ["echo", "x"]}'),
+        function=AssistantFunctionTool(name="vcs_diff", arguments='{"path": ""}'),
     )
     await render_events(
         _aiter(
@@ -103,6 +103,14 @@ async def test_pretty_read_file_done(capsys: pytest.CaptureFixture[str]) -> None
     assert "[tool ok]" not in out
 
 
+async def test_pretty_read_file_numbered_no_range(capsys: pytest.CaptureFixture[str]) -> None:
+    """Numbered reads carry no L header, so the summary falls back to ``(done)``."""
+    content = "    1|one\n    2|two\n"
+    await render_events(_aiter([_read_call('{"path": "a.txt", "with_lineno": true}'), _result(content)]))
+    out = capsys.readouterr().out
+    assert "* Read 'a.txt' (done)" in out
+
+
 async def test_pretty_read_file_statuses(capsys: pytest.CaptureFixture[str]) -> None:
     cases = [
         ("error: file not found: a.txt", "(file not found)"),
@@ -116,6 +124,44 @@ async def test_pretty_read_file_statuses(capsys: pytest.CaptureFixture[str]) ->
         assert f"* Read 'a.txt' {status}" in out, f"status {status} not rendered for {content!r}"
 
 
+def _tree_call(args_json: str) -> ToolCallEvent:
+    return ToolCallEvent(
+        tool_call=AssistantFunctionToolCall(
+            id="1",
+            function=AssistantFunctionTool(name="tree", arguments=args_json),
+        )
+    )
+
+
+async def test_pretty_tree_markdown(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "- src/\n  - main.py\n  - nested/\n    - deep.txt\n- a.txt\n"
+    await render_events(_aiter([_tree_call('{"path": "."}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Tree '.' (2 dirs, 3 files, depth 3)" in out
+    assert "[tool]" not in out
+
+
+async def test_pretty_tree_flat_omits_depth(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "src/\nsrc/main.py\na.txt\n… (5 more paths not shown)"
+    await render_events(_aiter([_tree_call('{"path": ".", "format": "flat"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Tree '.' (1 dirs, 2 files)" in out
+    assert "depth" not in out
+
+
+async def test_pretty_tree_decorated(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "src/\n├── main.py\n└── nested/\n    └── deep.txt\n"
+    await render_events(_aiter([_tree_call('{"path": "src", "format": "decorated"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Tree 'src' (1 dirs, 2 files, depth 2)" in out
+
+
+async def test_pretty_tree_error(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_tree_call('{"path": "nope"}'), _result("error: not a directory: nope")]))
+    out = capsys.readouterr().out
+    assert "* Tree 'nope' (error)" in out
+
+
 async def test_pretty_todo_push(capsys: pytest.CaptureFixture[str]) -> None:
     call = ToolCallEvent(
         tool_call=AssistantFunctionToolCall(
@@ -140,12 +186,12 @@ async def test_non_pretty_tool_keeps_old_style(capsys: pytest.CaptureFixture[str
     call = ToolCallEvent(
         tool_call=AssistantFunctionToolCall(
             id="3",
-            function=AssistantFunctionTool(name="run_argv", arguments='{"argv": ["ls"]}'),
+            function=AssistantFunctionTool(name="vcs_diff", arguments='{"path": ""}'),
         )
     )
-    await render_events(_aiter([call, _result("exit_code=0")]))
+    await render_events(_aiter([call, _result("diff --git a/x b/x")]))
     out = capsys.readouterr().out
-    assert "[tool] run_argv(" in out
+    assert "[tool] vcs_diff(" in out
     assert "[tool ok]" in out
 
 
@@ -210,3 +256,305 @@ def test_markdown_render_available_respects_plain_env(monkeypatch: pytest.Monkey
     monkeypatch.setenv("PLYNGENT_PLAIN", "1")
     assert markdown_render_available() is False
     monkeypatch.delenv("PLYNGENT_PLAIN", raising=False)
+
+
+async def test_pretty_verbose_shows_full_result(capsys: pytest.CaptureFixture[str]) -> None:
+    """Verbose mode prints the full tool result even for pretty tools."""
+    await render_events(
+        _aiter([_read_call('{"path": "a.txt"}'), _result("L1-4\none\ntwo\n")]),
+        verbose=True,
+    )
+    out = capsys.readouterr().out
+    assert "[tool ok]" in out
+    assert "L1-4\none\ntwo" in out
+    assert "* Read" not in out
+
+
+async def test_pretty_plain_output_has_no_ansi(capsys: pytest.CaptureFixture[str]) -> None:
+    """Pretty summaries are plain text when stdout is not a TTY."""
+    await render_events(_aiter([_read_call('{"path": "a.txt"}'), _result("L1-4\none\n")]))
+    out = capsys.readouterr().out
+    assert "\x1b[" not in out
+
+
+async def test_tool_result_preview_first_line_and_count(capsys: pytest.CaptureFixture[str]) -> None:
+    """Non-verbose preview shows the first line plus a line-count tail."""
+    set_markdown_enabled(False)
+    content = "first line\nsecond\nthird"
+    await render_events(_aiter([ToolResultEvent(message=ToolChatMessage(content=content, tool_call_id="1"))]))
+    out = capsys.readouterr().out
+    assert "[tool ok] first line (…2 more lines)" in out
+
+    await render_events(_aiter([ToolResultEvent(message=ToolChatMessage(content="only line", tool_call_id="2"))]))
+    out = capsys.readouterr().out
+    assert "[tool ok] only line" in out
+    assert "more" not in out
+
+    await render_events(_aiter([ToolResultEvent(message=ToolChatMessage(content="", tool_call_id="3"))]))
+    out = capsys.readouterr().out
+    assert "[tool ok] (no output)" in out
+    set_markdown_enabled(True)
+
+
+def _pretty_call(name: str, args_json: str) -> ToolCallEvent:
+    return ToolCallEvent(
+        tool_call=AssistantFunctionToolCall(
+            id="1",
+            function=AssistantFunctionTool(name=name, arguments=args_json),
+        )
+    )
+
+
+async def test_pretty_listdir(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "dir\tsrc\nfile\tREADME.md\nfile\tpyproject.toml\n"
+    await render_events(_aiter([_pretty_call("listdir", '{"path": "src"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* List 'src' (1 dirs, 2 files)" in out
+    assert "[tool]" not in out
+    assert "[tool ok]" not in out
+
+
+async def test_pretty_listdir_empty(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("listdir", '{"path": "src"}'), _result("(empty)")]))
+    out = capsys.readouterr().out
+    assert "* List 'src' (empty)" in out
+
+
+async def test_pretty_listdir_error(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("listdir", '{"path": "nope"}'), _result("error: not a directory: nope")]))
+    out = capsys.readouterr().out
+    assert "* List 'nope' (error: not a directory: nope)" in out
+
+
+async def test_pretty_glob(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "src/a.py\nsrc/b.py\n"
+    await render_events(_aiter([_pretty_call("glob_paths", '{"pattern": "**/*.py"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Glob '**/*.py' in '.' (2 paths)" in out
+
+
+async def test_pretty_glob_no_matches(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("glob_paths", '{"pattern": "**/*.rs"}'), _result("(no matches)")]))
+    out = capsys.readouterr().out
+    assert "* Glob '**/*.rs' in '.' (no matches)" in out
+
+
+async def test_pretty_glob_truncated(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "a\nb\n...[truncated at 200 matches]"
+    await render_events(_aiter([_pretty_call("glob_paths", '{"pattern": "*"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Glob '*' in '.' (2 paths)" in out
+
+
+async def test_pretty_grep(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "src/a.py:3: x = 1\nsrc/a.py:9: x = 2\nsrc/b.py:1: y = 3\n"
+    await render_events(_aiter([_pretty_call("grep_files", '{"pattern": "x"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Grep 'x' in '.' (3 matches in 2 files)" in out
+
+
+async def test_pretty_grep_no_matches(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("grep_files", '{"pattern": "zzz"}'), _result("(no matches)")]))
+    out = capsys.readouterr().out
+    assert "* Grep 'zzz' in '.' (no matches)" in out
+
+
+async def test_pretty_run_argv_success(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "exit_code=0\ntimed_out=false\ncwd=.\ncmd=git status --short\n--- stdout ---\n M src/foo.py\n--- stderr ---\n"
+    )
+    await render_events(_aiter([_pretty_call("run_argv", '{"argv": ["git", "status", "--short"]}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Run $ git status --short (exit code 0)" in out
+    assert "[tool]" not in out
+    assert "[tool ok]" not in out
+
+
+async def test_pretty_run_argv_failure(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "exit_code=1\ntimed_out=false\ncwd=.\ncmd=ls /nope\n--- stdout ---\n--- stderr ---\nls: cannot access '/nope'\n"
+    )
+    await render_events(_aiter([_pretty_call("run_argv", '{"argv": ["ls", "/nope"]}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Run $ ls /nope (exit code 1)" in out
+
+
+async def test_pretty_run_argv_timed_out(capsys: pytest.CaptureFixture[str]) -> None:
+    result = "exit_code=\ntimed_out=true\ncwd=.\ncmd=sleep 10\n--- stdout ---\n--- stderr ---\n"
+    await render_events(_aiter([_pretty_call("run_argv", '{"argv": ["sleep", "10"]}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Run $ sleep 10 (timed out)" in out
+
+
+async def test_pretty_run_argv_error(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(
+        _aiter([_pretty_call("run_argv", '{"argv": ["nope"]}'), _result("error: executable not found: 'nope'")])
+    )
+    out = capsys.readouterr().out
+    assert "* Run $ nope (error: executable not found: 'nope')" in out
+
+
+async def test_pretty_run_argv_batch_stopped(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "steps=3 ran=2 stop_on_error=true stopped_early=true\n"
+        "--- step 1 ---\nexit_code=1\ntimed_out=false\ncwd=.\ncmd=git status\n"
+        "pipe_out=false\nmix_stderr=false\n--- stdout ---\n--- stderr ---\n"
+        "--- step 2 ---\nexit_code=0\ntimed_out=false\ncwd=.\ncmd=git diff\n"
+        "pipe_out=false\nmix_stderr=false\n--- stdout ---\n--- stderr ---\n"
+        "--- summary ---\nlast_exit=1\n"
+    )
+    await render_events(_aiter([_pretty_call("run_argv_batch", '{"steps": []}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Run batch (stopped early)" in out
+
+
+async def test_pretty_run_argv_batch_complete(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "steps=2 ran=2 stop_on_error=true stopped_early=false\n"
+        "--- step 1 ---\nexit_code=0\n--- stdout ---\n--- stderr ---\n"
+        "--- step 2 ---\nexit_code=0\n--- stdout ---\n--- stderr ---\n"
+        "--- summary ---\nlast_exit=0\n"
+    )
+    await render_events(_aiter([_pretty_call("run_argv_batch", '{"steps": []}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Run batch (done)" in out
+
+
+async def test_pretty_fetch(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "status=200\nmethod=GET\nfinal_url=https://example.com\ncontent_type=application/json\n"
+        "body_kind=json\nbytes=1229\ntruncated=false\nredirects=0\nsecurity=public\n--- body ---\n{...}\n"
+    )
+    await render_events(_aiter([_pretty_call("fetch", '{"url": "https://example.com"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Fetch GET https://example.com (200)" in out
+    assert "[tool]" not in out
+
+
+async def test_pretty_fetch_error_status(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "status=404\nmethod=GET\nfinal_url=https://example.com/nope\ncontent_type=text/html\n"
+        "body_kind=html\nbytes=45\ntruncated=false\nredirects=0\nsecurity=public\n--- body ---\nNot found\n"
+    )
+    await render_events(_aiter([_pretty_call("fetch", '{"url": "https://example.com/nope"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Fetch GET https://example.com/nope (404)" in out
+
+
+async def test_pretty_fetch_truncated(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "status=200\nmethod=GET\nfinal_url=https://example.com\ncontent_type=text/plain\n"
+        "body_kind=text\nbytes=50000\ntruncated=true\nredirects=0\nsecurity=public\n--- body ---\n..."
+    )
+    await render_events(_aiter([_pretty_call("fetch", '{"url": "https://example.com"}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* Fetch GET https://example.com (200)" in out
+
+
+async def test_pretty_fetch_error(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(
+        _aiter([_pretty_call("fetch", '{"url": "https://example.com"}'), _result("error: fetch failed: boom")])
+    )
+    out = capsys.readouterr().out
+    assert "* Fetch GET https://example.com (error: fetch failed: boom)" in out
+
+
+async def test_pretty_mutators(capsys: pytest.CaptureFixture[str]) -> None:
+    cases = [
+        ("write_file", '{"path": "src/x.py"}', "wrote 120 characters to src/x.py", "* Write 'src/x.py' (120 chars)"),
+        (
+            "edit_replace",
+            '{"path": "src/a.py"}',
+            "replaced 1 occurrence in src/a.py ('x' → 'y')",
+            "* Edit 'src/a.py' (done)",
+        ),
+        (
+            "edit_lineno",
+            '{"path": "src/a.py"}',
+            "replaced lines 3-5 (3 lines; first: 'pass') with 2 lines in src/a.py",
+            "* Edit 'src/a.py' (done)",
+        ),
+        (
+            "copy_path",
+            '{"src": "a.txt", "dst": "b.txt"}',
+            "copied file a.txt -> b.txt",
+            "* Copy 'a.txt' → 'b.txt' (done)",
+        ),
+        ("move_path", '{"src": "src", "dst": "dst"}', "moved directory src -> dst", "* Move 'src' → 'dst' (done)"),
+        ("delete_path", '{"path": "tmp/x.txt"}', "deleted file tmp/x.txt", "* Delete 'tmp/x.txt' (done)"),
+    ]
+    for name, args, content, expected in cases:
+        await render_events(_aiter([_pretty_call(name, args), _result(content)]))
+        out = capsys.readouterr().out
+        assert expected in out, f"{name}: expected {expected!r} in {out!r}"
+        assert "[tool ok]" not in out
+
+
+async def test_pretty_mutator_error(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(
+        _aiter([_pretty_call("copy_path", '{"src": "x", "dst": "y"}'), _result("error: source does not exist: x")])
+    )
+    out = capsys.readouterr().out
+    assert "* Copy 'x' → 'y' (error: source does not exist: x)" in out
+
+
+async def test_pretty_vcs_status_done(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("vcs_status", "{}"), _result("(clean)")]))
+    out = capsys.readouterr().out
+    assert "* VCS Status (done)" in out
+    assert "[tool]" not in out
+
+
+async def test_pretty_vcs_status_error(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(
+        _aiter(
+            [
+                _pretty_call("vcs_status", "{}"),
+                _result("error: no supported VCS detected under workspace (currently: git)"),
+            ]
+        )
+    )
+    out = capsys.readouterr().out
+    assert "* VCS Status (error: no supported VCS detected under workspace (currently: git))" in out
+
+
+async def test_pretty_vcs_log_count(capsys: pytest.CaptureFixture[str]) -> None:
+    result = (
+        "5436457 2026-08-15 worldmozara core/tools: allow edit_lineno append\nabc1234 2026-08-14 worldmozara cli: fix\n"
+    )
+    await render_events(_aiter([_pretty_call("vcs_log", '{"limit": 2}'), _result(result)]))
+    out = capsys.readouterr().out
+    assert "* VCS Log (2 commits)" in out
+
+
+async def test_pretty_vcs_log_single(capsys: pytest.CaptureFixture[str]) -> None:
+    content = "abc1234 2026-08-14 worldmozara x\n"
+    await render_events(_aiter([_pretty_call("vcs_log", '{"limit": 1}'), _result(content)]))
+    out = capsys.readouterr().out
+    assert "* VCS Log (1 commit)" in out
+
+
+async def test_pretty_vcs_log_no_commits(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("vcs_log", "{}"), _result("(no commits)")]))
+    out = capsys.readouterr().out
+    assert "* VCS Log (no commits)" in out
+
+
+async def test_pretty_wait_waited(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("wait", '{"duration": 5}'), _result("waited 5s")]))
+    out = capsys.readouterr().out
+    assert "* Wait (5s)" in out
+    assert "[tool]" not in out
+
+
+async def test_pretty_wait_disturbed(capsys: pytest.CaptureFixture[str]) -> None:
+    await render_events(_aiter([_pretty_call("wait", '{"duration": 30}'), _result("disturbed by user: ship it")]))
+    out = capsys.readouterr().out
+    assert "* Wait (disturbed)" in out
+
+
+async def test_pretty_wait_error(capsys: pytest.CaptureFixture[str]) -> None:
+    content = "error: duration must not be negative"
+    await render_events(_aiter([_pretty_call("wait", '{"duration": -1}'), _result(content)]))
+    out = capsys.readouterr().out
+    assert "* Wait (error: duration must not be negative)" in out

tests/test_cli/test_grants_cmd.py

@@ -0,0 +1,156 @@
+"""CLI slash ``/grants``, session hydrate/persist, and the access confirm hook."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import pytest
+import tomlkit
+
+from plyngent.cli.slash import handle_slash
+from plyngent.cli.state import ReplState
+from plyngent.config.models import DatabaseConfig, OpenAIProvider
+from plyngent.config.store import ConfigStore
+from plyngent.memory import MemoryStore
+from plyngent.prompting import NonInteractiveBackend, temporary_backend
+from plyngent.tools import AccessMode, grant_session_access
+from plyngent.tools.access import AccessDecision
+
+if TYPE_CHECKING:
+    from collections.abc import AsyncIterator
+    from pathlib import Path
+
+
+async def _new_state(
+    tmp_path: Path,
+    *,
+    document: object | None = None,
+) -> tuple[ReplState, MemoryStore]:
+    memory = await MemoryStore.open(DatabaseConfig())
+    provider = OpenAIProvider(access_key_or_token="sk-test")
+    config = ConfigStore(
+        path=tmp_path / "plyngent.toml",
+        document=tomlkit.document() if document is None else document,
+    )
+    config.providers = {"local": provider}
+    state = ReplState(
+        config=config,
+        memory=memory,
+        workspace=tmp_path,
+        provider_name="local",
+        provider=provider,
+        model="gpt-test",
+        tools_enabled=False,
+    )
+    await state.new_session("t")
+    return state, memory
+
+
+@pytest.fixture
+async def state(tmp_path: Path) -> AsyncIterator[ReplState]:
+    st, memory = await _new_state(tmp_path)
+    yield st
+    await memory.close()
+
+
+async def test_grants_list_empty(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    assert await handle_slash(state, "/grants") is True
+    assert "no directory-access grants" in capsys.readouterr().out
+
+
+async def test_grants_list_and_revoke_session(
+    state: ReplState,
+    tmp_path: Path,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    outside = (tmp_path.parent / "outside-grant").resolve()
+    outside.mkdir(exist_ok=True)
+    _ = grant_session_access(outside, AccessMode.READ, session=state.session_state)
+    state.instance_state.workspace.yolo_allow[outside] = AccessMode.EXEC
+    state.instance_state.workspace.config_allow[tmp_path] = AccessMode.READ
+
+    assert await handle_slash(state, "/grants list") is True
+    out = capsys.readouterr().out
+    assert "directory-access grants (3)" in out
+    assert "session" in out
+    assert "process" in out
+    assert "config" in out
+
+    # Rows are ordered session, process, config.
+    assert await handle_slash(state, "/grants revoke 0") is True
+    assert "revoked" in capsys.readouterr().out
+    assert state.session_state.access_grants == {}
+    assert await state.memory.get_session_access_grants(state.session_id) == {}
+
+
+async def test_grants_revoke_all_keeps_config(
+    state: ReplState,
+    tmp_path: Path,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    outside = (tmp_path.parent / "outside-all").resolve()
+    outside.mkdir(exist_ok=True)
+    _ = grant_session_access(outside, AccessMode.READ, session=state.session_state)
+    state.instance_state.workspace.yolo_allow[outside] = AccessMode.WRITE
+    state.instance_state.workspace.config_allow[tmp_path] = AccessMode.READ
+
+    assert await handle_slash(state, "/grants revoke all") is True
+    assert "config grants unchanged" in capsys.readouterr().out
+    assert state.session_state.access_grants == {}
+    assert state.instance_state.workspace.yolo_allow == {}
+    assert state.instance_state.workspace.config_allow == {tmp_path: AccessMode.READ}
+
+
+async def test_grants_revoke_config_points_at_toml(
+    state: ReplState,
+    tmp_path: Path,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    state.instance_state.workspace.config_allow[tmp_path] = AccessMode.READ
+    assert await handle_slash(state, "/grants revoke 0") is True
+    assert "edit [agent].allow_paths" in capsys.readouterr().out
+    assert state.instance_state.workspace.config_allow == {tmp_path: AccessMode.READ}
+
+
+async def test_grants_revoke_bad_index(
+    state: ReplState,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    assert await handle_slash(state, "/grants revoke 99") is True
+    assert "no grant at index 99" in capsys.readouterr().err
+
+
+async def test_persist_and_load_roundtrip(state: ReplState, tmp_path: Path) -> None:
+    outside = (tmp_path.parent / "outside-hydrate").resolve()
+    outside.mkdir(exist_ok=True)
+    _ = grant_session_access(outside, AccessMode.WRITE, session=state.session_state)
+    await state.persist_access_grants()
+    state.session_state.access_grants.clear()
+    await state.load_access_grants()
+    assert state.session_state.access_grants == {outside: AccessMode.WRITE}
+
+
+def test_yolo_hook_auto_approves_as_process_grant(state: ReplState, tmp_path: Path) -> None:
+    state.set_yolo("on")
+    decision = state.directory_access_confirm_hook(tmp_path, AccessMode.EXEC, "", 30.0)
+    assert decision == AccessDecision(AccessMode.EXEC, persist=False)
+
+
+def test_default_hook_denies_noninteractive(state: ReplState, tmp_path: Path) -> None:
+    with temporary_backend(NonInteractiveBackend()):
+        assert state.directory_access_confirm_hook(tmp_path, AccessMode.READ, "", 1.0) is None
+
+
+async def test_config_allow_paths_installed(
+    tmp_path: Path,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    outside = (tmp_path.parent / "outside-config").resolve()
+    outside.mkdir(exist_ok=True)
+    document = tomlkit.parse(f'[agent]\nallow_paths = {{ "{outside}" = "read", "/does/not/exist" = "read" }}\n')
+    state, memory = await _new_state(tmp_path, document=document)
+    try:
+        assert state.instance_state.workspace.config_allow == {outside: AccessMode.READ}
+        assert "ignored allow_paths entries" in capsys.readouterr().err
+    finally:
+        await memory.close()

tests/test_cli/test_interrupt.py

@@ -16,6 +16,8 @@ from plyngent.cli.interrupt import (
 )
 from plyngent.cli.limits import prompt_continue_limit, prompt_continue_limit_async
 from plyngent.cli.retry import run_cancellable
+from plyngent.prompting import temporary_backend
+from tests.test_prompting import ScriptedBackend
 
 if TYPE_CHECKING:
     pass
@@ -39,12 +41,16 @@ def test_nested_pause_depth() -> None:
 
 
 def test_prompt_continue_limit_under_pause(monkeypatch: pytest.MonkeyPatch) -> None:
-    def _confirm(*_a: object, **_k: object) -> bool:
-        assert allow_task_cancel() is False
-        return True
+    backend = ScriptedBackend(["y"])
 
-    monkeypatch.setattr("click.confirm", _confirm)
-    assert prompt_continue_limit("too many rounds") is True
+    def _read_line(prompt: str, *, default: str | None = None, completions: object = None) -> str:
+        del prompt, default, completions
+        assert allow_task_cancel() is False
+        return "y"
+
+    monkeypatch.setattr(backend, "read_line", _read_line)
+    with temporary_backend(backend):
+        assert prompt_continue_limit("too many rounds") is True
 
 
 async def test_run_in_prompt_thread_pauses_cancel() -> None:
@@ -60,11 +66,9 @@ async def test_run_in_prompt_thread_pauses_cancel() -> None:
 
 
 async def test_prompt_continue_limit_async(monkeypatch: pytest.MonkeyPatch) -> None:
-    def _confirm(*_a: object, **_k: object) -> bool:
-        return True
-
-    monkeypatch.setattr("click.confirm", _confirm)
-    assert await prompt_continue_limit_async("too many rounds") is True
+    del monkeypatch
+    with temporary_backend(ScriptedBackend(["y"])):
+        assert await prompt_continue_limit_async("too many rounds") is True
 
 
 async def test_sigint_cancels_after_prompt_pause() -> None:

tests/test_cli/test_limits.py

@@ -1,28 +1,106 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
+import pytest
+
 from plyngent.cli.limits import (
+    auto_continue_enabled,
     format_tool_confirm_box,
     install_cli_limit_hooks,
     prompt_confirm_tool,
     prompt_continue_limit,
+    reset_auto_continue,
+    reset_auto_continue_turn,
+    set_auto_continue_default,
 )
-from plyngent.prompting import get_prompt_backend, temporary_backend
+from plyngent.prompting import NonInteractiveBackend, get_prompt_backend, temporary_backend
 from plyngent.tools.process.pty_session import PtyManager
 from tests.test_prompting import ScriptedBackend
 
+if TYPE_CHECKING:
+    from collections.abc import Iterator
+
+
+@pytest.fixture
+def clean_auto_continue() -> Iterator[None]:
+    reset_auto_continue()
+    yield
+    reset_auto_continue()
+
 
 def test_prompt_continue_limit_yes() -> None:
-    backend = ScriptedBackend([], confirms=[True])
+    backend = ScriptedBackend(["y"])
+    with temporary_backend(backend):
+        assert prompt_continue_limit("hit a wall") is True
+
+
+def test_prompt_continue_limit_default_yes() -> None:
+    backend = ScriptedBackend([])
     with temporary_backend(backend):
         assert prompt_continue_limit("hit a wall") is True
 
 
 def test_prompt_continue_limit_no() -> None:
-    backend = ScriptedBackend([], confirms=[False])
+    backend = ScriptedBackend(["n"])
     with temporary_backend(backend):
         assert prompt_continue_limit("hit a wall") is False
 
 
+def test_prompt_continue_limit_yyy_sets_turn_skip(clean_auto_continue: None) -> None:
+    del clean_auto_continue
+    backend = ScriptedBackend(["yyy"])
+    with temporary_backend(backend):
+        assert prompt_continue_limit("hit a wall") is True
+        assert auto_continue_enabled() is True
+        # No further prompt: the script is empty and must not be consumed.
+        assert prompt_continue_limit("hit a wall again") is True
+
+
+def test_reset_auto_continue_turn_clears_yyy(clean_auto_continue: None) -> None:
+    del clean_auto_continue
+    with temporary_backend(ScriptedBackend(["yyy"])):
+        assert prompt_continue_limit("limit") is True
+    reset_auto_continue_turn()
+    assert auto_continue_enabled() is False
+    with temporary_backend(ScriptedBackend(["n"])):
+        assert prompt_continue_limit("limit") is False
+
+
+def test_auto_continue_default_short_circuits_prompt(clean_auto_continue: None) -> None:
+    del clean_auto_continue
+    set_auto_continue_default(enabled=True)
+    assert auto_continue_enabled() is True
+    with temporary_backend(NonInteractiveBackend()):
+        assert prompt_continue_limit("limit") is True
+
+
+def test_prompt_continue_limit_noninteractive_denies() -> None:
+    with temporary_backend(NonInteractiveBackend()):
+        assert prompt_continue_limit("limit") is False
+
+
+def test_setup_hooks_installs_pty_hook_for_auto_continue(clean_auto_continue: None) -> None:
+    del clean_auto_continue
+    from plyngent.cli.app import _setup_hooks
+
+    _setup_hooks(interactive=False, auto_continue=True)
+    assert PtyManager._limit_continue is not None
+    _setup_hooks(interactive=False, auto_continue=False)
+    assert PtyManager._limit_continue is None
+
+
+def test_pty_offer_raise_uses_auto_continue(clean_auto_continue: None) -> None:
+    del clean_auto_continue
+    PtyManager.set_limit_continue_hook(prompt_continue_limit)
+    set_auto_continue_default(enabled=True)
+    try:
+        with temporary_backend(NonInteractiveBackend()):
+            assert PtyManager._offer_raise("PTY session limit reached") is True
+    finally:
+        PtyManager.set_limit_continue_hook(None)
+
+
 def test_prompt_confirm_tool_default_deny() -> None:
     backend = ScriptedBackend([], confirms=[False])
     with temporary_backend(backend):
@@ -54,3 +132,37 @@ def test_policy_confirm_noninteractive_denies() -> None:
 
     with temporary_backend(NonInteractiveBackend()):
         assert prompt_policy_command_confirm("sudo", ["sudo", "id"], 1.0) is False
+
+
+def test_directory_access_prompt_noninteractive_denies() -> None:
+    from pathlib import Path
+
+    from plyngent.cli.limits import prompt_directory_access_confirm
+    from plyngent.prompting import NonInteractiveBackend
+    from plyngent.tools.workspace import AccessMode
+
+    with temporary_backend(NonInteractiveBackend()):
+        assert prompt_directory_access_confirm(Path("/tmp"), AccessMode.READ, "why", 1.0) is None
+
+
+def test_directory_access_prompt_yes_and_level(monkeypatch: pytest.MonkeyPatch) -> None:
+    from pathlib import Path
+
+    from plyngent.cli import limits
+    from plyngent.tools.access import AccessDecision
+    from plyngent.tools.workspace import AccessMode
+
+    target = Path("/tmp")
+    with temporary_backend(ScriptedBackend([])):
+        monkeypatch.setattr(limits, "_read_yes_no_line_with_timeout", lambda _timeout: "y\n")
+        assert limits.prompt_directory_access_confirm(target, AccessMode.READ, "why", 30.0) == AccessDecision(
+            AccessMode.READ
+        )
+        monkeypatch.setattr(limits, "_read_yes_no_line_with_timeout", lambda _timeout: "exec\n")
+        assert limits.prompt_directory_access_confirm(target, AccessMode.READ, "why", 30.0) == AccessDecision(
+            AccessMode.EXEC
+        )
+        monkeypatch.setattr(limits, "_read_yes_no_line_with_timeout", lambda _timeout: "n\n")
+        assert limits.prompt_directory_access_confirm(target, AccessMode.READ, "why", 30.0) is None
+        monkeypatch.setattr(limits, "_read_yes_no_line_with_timeout", lambda _timeout: None)
+        assert limits.prompt_directory_access_confirm(target, AccessMode.READ, "why", 30.0) is None

tests/test_cli/test_mcp_cmd.py

@@ -0,0 +1,230 @@
+"""CLI slash ``/mcp`` command and MCP wiring in ``ReplState``."""
+
+from __future__ import annotations
+
+import json
+import sys
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import pytest
+import tomlkit
+
+from plyngent.cli.slash import handle_slash
+from plyngent.cli.state import ReplState
+from plyngent.config.models import DatabaseConfig, McpConfig, McpServerConfig, OpenAIProvider
+from plyngent.config.store import ConfigStore
+from plyngent.memory import MemoryStore
+from plyngent.runtime.mcp_client import McpManager
+
+if TYPE_CHECKING:
+    from collections.abc import AsyncIterator
+
+_FAKE_SERVER = Path(__file__).parent.parent / "test_runtime" / "mcp_fake_server.py"
+
+
+def _server_config(**overrides: object) -> McpServerConfig:
+    base: dict[str, object] = {
+        "command": sys.executable,
+        "args": [str(_FAKE_SERVER)],
+        "timeout": 5.0,
+    }
+    return McpServerConfig(**{**base, **overrides})  # type: ignore[arg-type]
+
+
+@pytest.fixture
+async def state(tmp_path: Path) -> AsyncIterator[ReplState]:
+    memory = await MemoryStore.open(DatabaseConfig())
+    provider = OpenAIProvider(access_key_or_token="sk-test")
+    config = ConfigStore(path=tmp_path / "plyngent.toml", document=tomlkit.document())
+    config.providers = {"local": provider}
+    st = ReplState(
+        config=config,
+        memory=memory,
+        workspace=tmp_path,
+        provider_name="local",
+        provider=provider,
+        model="gpt-test",
+        tools_enabled=False,
+    )
+    await st.new_session("t")
+    yield st
+    await memory.close()
+
+
+async def test_slash_mcp_list_without_manager(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    assert await handle_slash(state, "/mcp") is True
+    assert "no servers configured" in capsys.readouterr().out
+    assert await handle_slash(state, "/mcp list") is True
+    assert "no servers configured" in capsys.readouterr().out
+
+
+async def test_slash_mcp_list_statuses(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    manager = McpManager(McpConfig(servers={"fake": _server_config()}, disable=[]))
+    await manager.ensure_started()
+    state.mcp_manager = manager
+    try:
+        assert await handle_slash(state, "/mcp list") is True
+        out = capsys.readouterr().out
+        assert "fake" in out
+        assert "connected" in out
+        assert "tools=3" in out
+    finally:
+        await manager.aclose()
+
+
+async def test_slash_mcp_reconnect_connects_new_config(
+    state: ReplState,
+    capsys: pytest.CaptureFixture[str],
+    tmp_path: Path,
+) -> None:
+    # The fixture's config file does not exist yet; write one with an MCP server.
+    payload = (
+        "[mcp.servers.fake]\n"
+        f"command = {json.dumps(sys.executable)}\n"
+        f"args = [{json.dumps(str(_FAKE_SERVER))}]\n"
+        "timeout = 5.0\n"
+    )
+    _ = (tmp_path / "plyngent.toml").write_text(payload, encoding="utf-8")
+    assert await handle_slash(state, "/mcp reconnect") is True
+    try:
+        assert state.mcp_manager is not None
+        statuses = state.mcp_manager.statuses()
+        assert [name for name, _, _ in statuses] == ["fake"]
+        assert statuses[0][1] == "connected"
+        assert statuses[0][2] == 3
+        out = capsys.readouterr().out
+        assert "tools=off" in out
+        assert "fake" in out
+    finally:
+        if state.mcp_manager is not None:
+            await state.mcp_manager.aclose()
+
+
+async def test_mcp_tools_registered_on_tools_rebuild(state: ReplState) -> None:
+    manager = McpManager(McpConfig(servers={"fake": _server_config()}, disable=[]))
+    await manager.ensure_started()
+    state.mcp_manager = manager
+    try:
+        from plyngent.tools.catalog import catalog_scope
+
+        state.tools_enabled = True
+        with catalog_scope(empty=True):
+            state.rebuild_client()
+        registry = state.agent.tools
+        assert registry is not None
+        assert registry.get("mcp__fake__echo") is not None
+        assert registry.get("mcp__fake__fail") is not None
+        # Handler proxies to the live server subprocess.
+        out = await registry.execute("mcp__fake__echo", '{"text": "hi"}')
+        assert out == "echo: hi"
+    finally:
+        await manager.aclose()
+
+
+async def test_slash_mcp_list_shows_instructions(
+    state: ReplState,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    guidance = "Prefer `echo` for repeating text back."
+    manager = McpManager(
+        McpConfig(
+            servers={
+                "fake": _server_config(env={"PLYNGENT_MCP_FAKE_INSTRUCTIONS": guidance}),
+            },
+            disable=[],
+        )
+    )
+    await manager.ensure_started()
+    state.mcp_manager = manager
+    try:
+        assert await handle_slash(state, "/mcp list") is True
+        out = capsys.readouterr().out
+        assert f"instructions ({len(guidance)} chars)" in out
+        assert guidance in out
+    finally:
+        await manager.aclose()
+
+
+async def _make_tools_state(
+    tmp_path: Path,
+    *,
+    agent_toml: str,
+    manager: McpManager,
+) -> tuple[ReplState, MemoryStore]:
+    """ReplState with tools on + a started MCP manager (agent built from TOML)."""
+    memory = await MemoryStore.open(DatabaseConfig())
+    provider = OpenAIProvider(access_key_or_token="sk-test")
+    document = tomlkit.parse(agent_toml) if agent_toml else tomlkit.document()
+    config = ConfigStore(path=tmp_path / "plyngent.toml", document=document)
+    config.providers = {"local": provider}
+    st = ReplState(
+        config=config,
+        memory=memory,
+        workspace=tmp_path,
+        provider_name="local",
+        provider=provider,
+        model="gpt-test",
+        tools_enabled=True,
+        mcp_manager=manager,
+    )
+    return st, memory
+
+
+async def test_mcp_instructions_folded_into_agent_system_prompt(tmp_path: Path) -> None:
+    from plyngent.tools.catalog import catalog_scope
+
+    guidance = "Prefer `echo` for repeating text back to the user."
+    manager = McpManager(
+        McpConfig(
+            servers={
+                "fake": _server_config(env={"PLYNGENT_MCP_FAKE_INSTRUCTIONS": guidance}),
+            },
+            disable=[],
+        )
+    )
+    await manager.ensure_started()
+    try:
+        with catalog_scope(empty=True):
+            state, memory = await _make_tools_state(tmp_path, agent_toml="", manager=manager)
+        try:
+            prompt = state.agent.system_prompt
+            assert prompt is not None
+            assert "MCP server 'fake' instructions:" in prompt
+            assert guidance in prompt
+        finally:
+            await memory.close()
+    finally:
+        await manager.aclose()
+
+
+async def test_mcp_instructions_flag_off_skips_server_text(tmp_path: Path) -> None:
+    from plyngent.tools.catalog import catalog_scope
+
+    guidance = "Prefer `echo` for repeating text back to the user."
+    manager = McpManager(
+        McpConfig(
+            servers={
+                "fake": _server_config(env={"PLYNGENT_MCP_FAKE_INSTRUCTIONS": guidance}),
+            },
+            disable=[],
+        )
+    )
+    await manager.ensure_started()
+    try:
+        with catalog_scope(empty=True):
+            state, memory = await _make_tools_state(
+                tmp_path,
+                agent_toml="[agent]\nmcp_instructions = false\n",
+                manager=manager,
+            )
+        try:
+            prompt = state.agent.system_prompt
+            assert prompt is not None
+            assert guidance not in prompt
+            assert "MCP server" not in prompt
+            assert "### Workspace" in prompt  # host tool playbook still composed
+        finally:
+            await memory.close()
+    finally:
+        await manager.aclose()

tests/test_cli/test_repl_commands.py

@@ -94,6 +94,32 @@ async def test_help_and_clear(state: ReplState) -> None:
     assert state.agent.messages == []
 
 
+async def test_auto_continue_limits_installs_on_limit(tmp_path: Path) -> None:
+    from plyngent.cli.limits import auto_continue_enabled, reset_auto_continue
+
+    memory = await MemoryStore.open(DatabaseConfig())
+    provider = OpenAIProvider(access_key_or_token="sk-test")
+    config = ConfigStore(path=tmp_path / "plyngent.toml", document=tomlkit.document())
+    config.providers = {"local": provider}
+    try:
+        st = ReplState(
+            config=config,
+            memory=memory,
+            workspace=tmp_path,
+            provider_name="local",
+            provider=provider,
+            model="gpt-test",
+            tools_enabled=False,
+            interactive_limits=False,
+            auto_continue_limits=True,
+        )
+        assert auto_continue_enabled() is True
+        assert st.agent.on_limit is not None
+    finally:
+        reset_auto_continue()
+        await memory.close()
+
+
 async def test_help_command_usage_line(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
     assert await handle_slash(state, "/help compact") is True
     out = capsys.readouterr().out
@@ -633,3 +659,108 @@ async def test_repl_second_ctrl_c_after_cancel_returns_to_prompt(
     assert calls["reads"] == 4  # three entries + EOF
     assert calls["echoes"] == 3  # the interrupting echo still counted, loop survived
     assert "interrupted" in capsys.readouterr().out
+
+
+async def test_btw_default_read_falls_back_when_tools_off(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    """Bare /btw (default --tools=read) still works under /tools off: no tools."""
+    assert state.tools_enabled is False
+    state.agent.stream = False  # DummyClient only completes via non-stream path
+    assert await handle_slash(state, "/btw hello") is True
+    out = capsys.readouterr().out
+    assert "btw: hello" in out
+    assert "btw done" in out
+    assert "error" not in out
+
+
+async def test_btw_explicit_tools_errors_when_off(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    """Explicitly requesting read/full tools while they are off is an error."""
+    state.agent.stream = False  # DummyClient only completes via non-stream path
+    assert await handle_slash(state, "/btw --tools read q") is True
+    assert "error: --tools requires tools on" in capsys.readouterr().out
+    assert await handle_slash(state, "/btw --tools full q") is True
+    assert "error: --tools requires tools on" in capsys.readouterr().out
+    # Explicit no is fine.
+    assert await handle_slash(state, "/btw --tools no q") is True
+    out = capsys.readouterr().out
+    assert "btw done" in out
+    assert "error" not in out
+
+
+async def test_btw_read_mode_wires_read_only_clone(
+    state: ReplState,
+    monkeypatch: pytest.MonkeyPatch,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    """--tools=read passes a read-only clone + read-only context + main session."""
+
+    from plyngent.agent import ToolRegistry, ToolTag, tool
+    from plyngent.tools.context import is_read_only_context
+
+    @tool(tags=ToolTag.LOCAL | ToolTag.READ_ONLY, register=False)
+    async def ro_tool() -> str:
+        return "ro"
+
+    @tool(tags=ToolTag.LOCAL, register=False)
+    async def w_tool() -> str:
+        return "w"
+
+    state.tools_enabled = True
+    state.agent.tools = ToolRegistry([ro_tool, w_tool], auto_bind_state=True)
+    captured: dict[str, object] = {}
+
+    async def fake_run_aside(_text: str, **kwargs: object) -> AsyncIterator[object]:
+        captured["tools"] = kwargs.get("tools")
+        captured["session_state"] = kwargs.get("session_state")
+        captured["read_only"] = is_read_only_context()
+        if False:
+            yield None
+
+    monkeypatch.setattr(state.agent, "run_aside", fake_run_aside)
+
+    assert await handle_slash(state, "/btw --tools read hi") is True
+    assert "btw done" in capsys.readouterr().out
+
+    tools = captured["tools"]
+    assert isinstance(tools, ToolRegistry)
+    assert {t.name for t in tools.definitions()} == {"ro_tool"}
+    assert captured["session_state"] is state.session_state
+    assert captured["read_only"] is True
+
+
+async def test_btw_full_mode_clones_full_registry(
+    state: ReplState,
+    monkeypatch: pytest.MonkeyPatch,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    """--tools=full keeps the whole registry with a fresh session, no context."""
+
+    from plyngent.agent import ToolRegistry, ToolTag, tool
+    from plyngent.tools.context import is_read_only_context
+
+    @tool(tags=ToolTag.LOCAL | ToolTag.READ_ONLY, register=False)
+    async def ro_tool() -> str:
+        return "ro"
+
+    @tool(tags=ToolTag.LOCAL, register=False)
+    async def w_tool() -> str:
+        return "w"
+
+    state.tools_enabled = True
+    state.agent.tools = ToolRegistry([ro_tool, w_tool], auto_bind_state=True)
+    captured: dict[str, object] = {}
+
+    async def fake_run_aside(_text: str, **kwargs: object) -> AsyncIterator[object]:
+        captured["tools"] = kwargs.get("tools")
+        captured["session_state"] = kwargs.get("session_state")
+        captured["read_only"] = is_read_only_context()
+        if False:
+            yield None
+
+    monkeypatch.setattr(state.agent, "run_aside", fake_run_aside)
+
+    assert await handle_slash(state, "/btw --tools full hi") is True
+    assert "btw done" in capsys.readouterr().out
+
+    assert captured["tools"] is True
+    assert captured["session_state"] is not state.session_state
+    assert captured["read_only"] is False

tests/test_cli/test_retry.py

@@ -30,6 +30,8 @@ from plyngent.memory import MemoryStore
 if TYPE_CHECKING:
     from collections.abc import AsyncIterator
 
+    from plyngent.agent import AgentEvent
+
 
 def test_default_retry_delays_schedule() -> None:
     assert DEFAULT_MAX_AUTO_RETRIES == 10
@@ -296,6 +298,43 @@ async def test_second_ctrl_c_during_retry_announce_stays_benign(
     assert await _wait_for_retry(1, 3, 0.01) is True
 
 
+async def test_turn_boundaries_reset_auto_continue() -> None:
+    from plyngent.cli.limits import (
+        auto_continue_enabled,
+        prompt_continue_limit,
+        reset_auto_continue,
+    )
+    from plyngent.prompting import temporary_backend
+    from tests.test_prompting import ScriptedBackend
+
+    reset_auto_continue()
+    try:
+        with temporary_backend(ScriptedBackend(["yyy"])):
+            assert prompt_continue_limit("limit") is True
+        assert auto_continue_enabled() is True
+
+        store = await MemoryStore.open(DatabaseConfig())
+        try:
+            session = await store.create_session(name="t")
+            client = FlakyClient(fail_times=0)
+            agent = ChatAgent(client, model="m", memory=store, session_id=session.sid)
+            seen: list[bool] = []
+
+            async def starter() -> AsyncIterator[AgentEvent]:
+                seen.append(auto_continue_enabled())
+                async for event in agent.run("hi"):
+                    yield event
+
+            ok = await run_turn_with_retries(agent, starter=starter, delays=())
+            assert ok is True
+            assert seen == [False]  # cleared before the turn starts
+            assert auto_continue_enabled() is False  # cleared after the turn ends
+        finally:
+            await store.close()
+    finally:
+        reset_auto_continue()
+
+
 async def test_manual_retry_after_exhausted(monkeypatch: pytest.MonkeyPatch) -> None:
     async def no_wait(_seconds: float) -> bool:
         return True

tests/test_config/test_agent_section.py

@@ -19,12 +19,15 @@ def test_agent_section_defaults(tmp_path: Path) -> None:
     store = load(path)
     assert store.agent_config.system_prompt == DEFAULT_SYSTEM_PROMPT
     assert store.agent_config.tool_directives == DEFAULT_TOOL_DIRECTIVES
+    assert store.agent_config.mcp_instructions is True
     assert "professional coding agent" in store.agent_config.system_prompt
     assert "### Workspace" in store.agent_config.tool_directives
     assert store.agent_config.max_tool_result_chars == 32_000
     assert store.agent_config.parallel_tools is True
     assert store.agent_config.confirm_destructive is True
     assert store.agent_config.path_denylist == []
+    assert store.agent_config.allow_paths == {}
+    assert store.agent_config.auto_continue_limits is False
     assert store.agent_config.max_context_tokens == 200_000
     assert store.plugins_config.enable == []
     assert store.plugins_config.disable == []
@@ -64,6 +67,9 @@ def test_compose_empty_combinations() -> None:
     assert compose_agent_system_content("Only persona", "") == "Only persona"
     assert compose_agent_system_content("", "Only tools") == "Only tools"
     assert compose_agent_system_content("Persona", "Tools") == "Persona\n\nTools"
+    assert compose_agent_system_content("", "", "") is None
+    assert compose_agent_system_content("Persona", "Tools", "Extra") == "Persona\n\nTools\n\nExtra"
+    assert compose_agent_system_content("Persona", "", "Extra") == "Persona\n\nExtra"
 
 
 def test_agent_section_parse(tmp_path: Path) -> None:
@@ -78,6 +84,7 @@ parallel_tools = false
 confirm_destructive = false
 path_denylist = ["/secrets/", ".ssh/"]
 max_context_tokens = 5000
+auto_continue_limits = true
 """,
         encoding="utf-8",
     )
@@ -89,6 +96,7 @@ max_context_tokens = 5000
     assert store.agent_config.confirm_destructive is False
     assert store.agent_config.path_denylist == ["/secrets/", ".ssh/"]
     assert store.agent_config.max_context_tokens == 5000
+    assert store.agent_config.auto_continue_limits is True
     composed = compose_agent_system_content(
         store.agent_config.system_prompt,
         store.agent_config.tool_directives,
@@ -158,6 +166,46 @@ tool_directives = ""
     )
 
 
+def test_agent_allow_paths_parse(tmp_path: Path) -> None:
+    path = tmp_path / "c.toml"
+    _ = path.write_text(
+        """
+[agent]
+allow_paths = { "/data/datasets" = "read", "/tmp/build" = "exec" }
+""",
+        encoding="utf-8",
+    )
+    store = load(path)
+    assert store.agent_config.allow_paths == {"/data/datasets": "read", "/tmp/build": "exec"}
+
+
+def test_agent_allow_paths_invalid_mode_falls_back(tmp_path: Path) -> None:
+    path = tmp_path / "c.toml"
+    _ = path.write_text(
+        """
+[agent]
+allow_paths = { "/data" = "sudo" }
+""",
+        encoding="utf-8",
+    )
+    store = load(path)
+    # Invalid field value resets the whole [agent] section to defaults.
+    assert store.agent_config.allow_paths == {}
+
+
+def test_agent_mcp_instructions_flag(tmp_path: Path) -> None:
+    path = tmp_path / "c.toml"
+    _ = path.write_text(
+        """
+[agent]
+mcp_instructions = false
+""",
+        encoding="utf-8",
+    )
+    store = load(path)
+    assert store.agent_config.mcp_instructions is False
+
+
 def test_plugins_section_parse(tmp_path: Path) -> None:
     path = tmp_path / "c.toml"
     _ = path.write_text(

tests/test_config/test_mcp_section.py

@@ -0,0 +1,66 @@
+"""[mcp] section parse: server definitions, disable gate, malformed fallback."""
+
+from __future__ import annotations
+
+from plyngent.config import load
+
+
+def test_mcp_defaults_and_parse(tmp_path) -> None:
+    path = tmp_path / "c.toml"
+    _ = path.write_text("", encoding="utf-8")
+    store = load(path)
+    assert store.mcp_config.servers == {}
+    assert store.mcp_config.disable == []
+
+    path.write_text(
+        """
+[mcp.servers.docs]
+command = "npx"
+args = ["-y", "@modelcontextprotocol/server-filesystem", "/tmp"]
+env = { RUST_LOG = "info" }
+timeout = 10.0
+read_only = true
+
+[mcp.servers.search]
+command = "uvx"
+args = ["mcp-server-fetch"]
+
+[mcp]
+disable = ["search"]
+""",
+        encoding="utf-8",
+    )
+    store = load(path)
+    mcp = store.mcp_config
+    assert set(mcp.servers) == {"docs", "search"}
+    docs = mcp.servers["docs"]
+    assert docs.command == "npx"
+    assert docs.args == ["-y", "@modelcontextprotocol/server-filesystem", "/tmp"]
+    assert docs.env == {"RUST_LOG": "info"}
+    assert docs.timeout == 10.0
+    assert docs.read_only is True
+    assert docs.url == ""
+    assert mcp.disable == ["search"]
+
+
+def test_mcp_malformed_section_falls_back_to_defaults(tmp_path) -> None:
+    path = tmp_path / "c.toml"
+    # Unknown section key.
+    path.write_text("[mcp]\nenabled = true\n", encoding="utf-8")
+    store = load(path)
+    assert store.mcp_config.servers == {}
+
+    # Unknown server key (typo).
+    path.write_text('[mcp.servers.docs]\ncmds = "npx"\n', encoding="utf-8")
+    store = load(path)
+    assert store.mcp_config.servers == {}
+
+    # Server entry is not a table.
+    path.write_text("[mcp]\nservers = 3\n", encoding="utf-8")
+    store = load(path)
+    assert store.mcp_config.servers == {}
+
+    # Empty server name.
+    path.write_text('[mcp.servers.""]\ncommand = "npx"\n', encoding="utf-8")
+    store = load(path)
+    assert store.mcp_config.servers == {}

tests/test_memory/test_store.py

@@ -34,6 +34,21 @@ async def test_create_session_uses_default_user(store: MemoryStore) -> None:
     assert session.uid == user.uid
 
 
+async def test_session_access_grants_roundtrip(store: MemoryStore) -> None:
+    session = await store.create_session(name="grants")
+    assert await store.get_session_access_grants(session.sid) == {}
+    _ = await store.update_session_access_grants(
+        session.sid,
+        {"/data/datasets": "read", "/tmp/build": "exec"},
+    )
+    assert await store.get_session_access_grants(session.sid) == {
+        "/data/datasets": "read",
+        "/tmp/build": "exec",
+    }
+    _ = await store.update_session_access_grants(session.sid, {})
+    assert await store.get_session_access_grants(session.sid) == {}
+
+
 async def test_session_context_usage_roundtrip(store: MemoryStore) -> None:
     session = await store.create_session(name="usage")
     row = await store.update_session_context_usage(
@@ -293,9 +308,9 @@ async def test_schema_migrations_stamp_version(tmp_path: object) -> None:
     db_path = tmp_path / "fresh.db"
     store = await MemoryStore.open(DatabaseConfig(url=str(db_path)))
     await store.close()
-    assert await _user_version(db_path) == 3
+    assert await _user_version(db_path) == 4
     columns = await _session_columns(db_path)
-    assert {"workspace", "provider_name", "model", "todo_stack", "last_prompt_tokens"} <= columns
+    assert {"workspace", "provider_name", "model", "todo_stack", "access_grants", "last_prompt_tokens"} <= columns
 
 
 async def test_legacy_db_migrated_to_latest(tmp_path: object) -> None:
@@ -311,9 +326,9 @@ async def test_legacy_db_migrated_to_latest(tmp_path: object) -> None:
     session = await store.create_session(name="migrated")
     await store.close()
 
-    assert await _user_version(db_path) == 3
+    assert await _user_version(db_path) == 4
     columns = await _session_columns(db_path)
-    assert {"workspace", "provider_name", "model", "todo_stack", "last_prompt_tokens"} <= columns
+    assert {"workspace", "provider_name", "model", "todo_stack", "access_grants", "last_prompt_tokens"} <= columns
     assert session.sid is not None
 
 
@@ -335,10 +350,10 @@ async def test_partially_migrated_legacy_db_noops_remaining_steps(tmp_path: obje
     session = await store.create_session(name="partial", workspace=tmp_path)
     await store.close()
 
-    assert await _user_version(db_path) == 3
+    assert await _user_version(db_path) == 4
     columns = await _session_columns(db_path)
     assert "workspace" in columns
-    assert {"provider_name", "model", "todo_stack", "last_prompt_tokens"} <= columns
+    assert {"provider_name", "model", "todo_stack", "access_grants", "last_prompt_tokens"} <= columns
     assert session.workspace is not None
 
 
@@ -350,8 +365,8 @@ async def test_stamped_db_skips_migrations_on_reopen(tmp_path: object) -> None:
     db_path = tmp_path / "stamped.db"
     store = await MemoryStore.open(DatabaseConfig(url=str(db_path)))
     await store.close()
-    assert await _user_version(db_path) == 3
+    assert await _user_version(db_path) == 4
 
     store = await MemoryStore.open(DatabaseConfig(url=str(db_path)))
     await store.close()
-    assert await _user_version(db_path) == 3
+    assert await _user_version(db_path) == 4

tests/test_runtime/mcp_fake_server.py

@@ -0,0 +1,103 @@
+"""Minimal MCP stdio server used by the client tests (echo + sleep tools).
+
+Set ``PLYNGENT_MCP_FAKE_INSTRUCTIONS`` (env) to have the server return that
+text as ``InitializeResult.instructions`` (usage guidance).
+"""
+
+from __future__ import annotations
+
+import json
+import os
+import sys
+
+_FAKE_INSTRUCTIONS = os.environ.get("PLYNGENT_MCP_FAKE_INSTRUCTIONS", "")
+
+
+def respond(request_id: int, result: object) -> None:
+    sys.stdout.write(json.dumps({"jsonrpc": "2.0", "id": request_id, "result": result}) + "\n")
+    sys.stdout.flush()
+
+
+def main() -> None:
+    for line in sys.stdin:
+        try:
+            payload = json.loads(line)
+        except json.JSONDecodeError:
+            continue
+        method = payload.get("method", "")
+        request_id = payload.get("id")
+        if request_id is None:
+            continue  # notification (notifications/initialized)
+        if method == "initialize":
+            result: dict[str, object] = {
+                "protocolVersion": "2025-06-18",
+                "capabilities": {"tools": {}},
+                "serverInfo": {"name": "fake-mcp", "version": "0.1.0"},
+            }
+            if _FAKE_INSTRUCTIONS:
+                result["instructions"] = _FAKE_INSTRUCTIONS
+            respond(int(request_id), result)
+        elif method == "tools/list":
+            respond(
+                int(request_id),
+                {
+                    "tools": [
+                        {
+                            "name": "echo",
+                            "description": "Echo the given text back.",
+                            "inputSchema": {
+                                "type": "object",
+                                "properties": {"text": {"type": "string"}},
+                                "required": ["text"],
+                            },
+                        },
+                        {
+                            "name": "fail",
+                            "description": "Always reports a tool error.",
+                            "inputSchema": {"type": "object", "properties": {}},
+                        },
+                        {
+                            "name": "slow",
+                            "description": "Sleeps past any client timeout.",
+                            "inputSchema": {"type": "object", "properties": {}},
+                        },
+                    ]
+                },
+            )
+        elif method == "tools/call":
+            name = (payload.get("params") or {}).get("name")
+            if name == "echo":
+                text = str((payload.get("params") or {}).get("arguments", {}).get("text", ""))
+                respond(
+                    int(request_id),
+                    {
+                        "content": [{"type": "text", "text": f"echo: {text}"}],
+                        "isError": False,
+                    },
+                )
+            elif name == "fail":
+                respond(
+                    int(request_id),
+                    {"content": [{"type": "text", "text": "boom"}], "isError": True},
+                )
+            else:
+                import time
+
+                time.sleep(5)
+                respond(int(request_id), {"content": [], "isError": False})
+        else:
+            sys.stdout.write(
+                json.dumps(
+                    {
+                        "jsonrpc": "2.0",
+                        "id": request_id,
+                        "error": {"code": -32601, "message": f"unknown method {method}"},
+                    }
+                )
+                + "\n"
+            )
+            sys.stdout.flush()
+
+
+if __name__ == "__main__":
+    main()

tests/test_runtime/test_mcp_client.py

@@ -0,0 +1,140 @@
+"""MCP stdio client + manager against the bundled fake server subprocess."""
+
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import pytest
+
+from plyngent.config.models import McpConfig, McpServerConfig
+from plyngent.runtime.mcp_client import (
+    McpConnectionError,
+    McpManager,
+    McpServerConnection,
+)
+
+_FAKE_SERVER = Path(__file__).parent / "mcp_fake_server.py"
+
+
+def _server_config(**overrides: object) -> McpServerConfig:
+    base: dict[str, object] = {
+        "command": sys.executable,
+        "args": [str(_FAKE_SERVER)],
+        "timeout": 5.0,
+    }
+    return McpServerConfig(**{**base, **overrides})  # type: ignore[arg-type]
+
+
+async def test_connection_handshake_lists_and_calls_tools() -> None:
+    connection = McpServerConnection("fake", _server_config())
+    await connection.start()
+    try:
+        assert connection.connected
+        assert connection.error is None
+        assert connection.instructions is None
+        assert [tool.name for tool in connection.tools] == ["echo", "fail", "slow"]
+        echo = connection.tools[0]
+        assert echo.description == "Echo the given text back."
+        assert echo.input_schema["type"] == "object"
+
+        result = await connection.call_tool("echo", {"text": "hello"})
+        assert result == "echo: hello"
+    finally:
+        await connection.aclose()
+
+
+async def test_initialize_captures_server_instructions() -> None:
+    guidance = "Use echo to repeat text back to the user."
+    connection = McpServerConnection(
+        "fake",
+        _server_config(env={"PLYNGENT_MCP_FAKE_INSTRUCTIONS": guidance}),
+    )
+    await connection.start()
+    try:
+        assert connection.connected
+        assert connection.instructions == guidance
+    finally:
+        await connection.aclose()
+
+
+async def test_tool_error_returns_error_text() -> None:
+    connection = McpServerConnection("fake", _server_config())
+    await connection.start()
+    try:
+        result = await connection.call_tool("fail", {})
+        assert result == "error: boom"
+    finally:
+        await connection.aclose()
+
+
+async def test_request_timeout_raises() -> None:
+    connection = McpServerConnection("fake", _server_config(timeout=0.2))
+    await connection.start()
+    try:
+        with pytest.raises(McpConnectionError, match="timed out"):
+            await connection.call_tool("slow", {})
+    finally:
+        await connection.aclose()
+
+
+async def test_spawn_failure_records_error() -> None:
+    connection = McpServerConnection("bad", _server_config(command="/nonexistent/plyngent-mcp-binary"))
+    await connection.start()
+    assert not connection.connected
+    assert connection.error is not None
+    assert "spawn" in connection.status
+    await connection.aclose()
+
+
+async def test_close_terminates_subprocess() -> None:
+    connection = McpServerConnection("fake", _server_config())
+    await connection.start()
+    proc = connection._proc
+    assert proc is not None
+    await connection.aclose()
+    assert connection._proc is None
+    assert proc.returncode is not None
+
+
+async def test_manager_start_status_and_call() -> None:
+    manager = McpManager(McpConfig(servers={"fake": _server_config()}, disable=[]))
+    await manager.ensure_started()
+    try:
+        assert [(name, status, count) for name, status, count in manager.statuses()] == [("fake", "connected", 3)]
+        assert manager.instructions() == []
+        assert await manager.call("fake", "echo", {"text": "hi"}) == "echo: hi"
+    finally:
+        await manager.aclose()
+    assert manager.statuses() == [("fake", "not started", 0)]
+
+
+async def test_manager_instructions_after_restart() -> None:
+    guidance = "Always answer with a haiku."
+    plain = McpManager(McpConfig(servers={"fake": _server_config()}, disable=[]))
+    await plain.ensure_started()
+    assert plain.instructions() == []
+    await plain.restart(
+        McpConfig(
+            servers={"fake": _server_config(env={"PLYNGENT_MCP_FAKE_INSTRUCTIONS": guidance})},
+            disable=[],
+        )
+    )
+    await plain.ensure_started()
+    try:
+        assert plain.instructions() == [("fake", guidance)]
+    finally:
+        await plain.aclose()
+
+
+async def test_manager_disable_and_restart() -> None:
+    manager = McpManager(McpConfig(servers={"fake": _server_config()}, disable=["fake"]))
+    await manager.ensure_started()
+    assert manager.connections() == []
+    with pytest.raises(McpConnectionError, match="not connected"):
+        await manager.call("fake", "echo", {})
+
+    await manager.restart(McpConfig(servers={"fake": _server_config()}, disable=[]))
+    await manager.ensure_started()
+    assert manager.statuses() == [("fake", "connected", 3)]
+    await manager.aclose()

tests/test_tools/test_access.py

@@ -0,0 +1,263 @@
+"""``request_directory_access`` tool and the grant stores."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import pytest
+
+from plyngent.agent import ToolTag
+from plyngent.tools import (
+    MAX_ACCESS_GRANTS,
+    AccessDecision,
+    AccessMode,
+    SessionState,
+    WorkspaceError,
+    active_workspace_policy,
+    get_directory_access_confirm_hook,
+    grant_session_access,
+    request_directory_access,
+    resolve_path,
+    set_config_access,
+    set_directory_access_confirm_hook,
+    set_path_denylist,
+)
+from plyngent.tools.context import bind_session
+from tests.test_tools.helpers import call_async
+
+if TYPE_CHECKING:
+    from collections.abc import Iterator
+    from pathlib import Path
+
+
+@pytest.fixture
+def session() -> Iterator[SessionState]:
+    state = SessionState()
+    with bind_session(state):
+        yield state
+
+
+def _never_called(*_args: object) -> AccessDecision | str | None:
+    msg = "confirm hook should not be called"
+    raise AssertionError(msg)
+
+
+def test_tool_tags_and_registry() -> None:
+    tags = request_directory_access.tags
+    assert tags & ToolTag.LOCAL
+    assert tags & ToolTag.INSTANCE_STATE
+    assert tags & ToolTag.SESSION_STATE
+    assert not (tags & ToolTag.READ_ONLY)
+    from plyngent.tools.catalog import default_tool_definitions
+
+    assert "request_directory_access" in {definition.name for definition in default_tool_definitions()}
+
+
+def test_hook_roundtrip(workspace: object, session: SessionState) -> None:
+    del workspace, session
+    assert get_directory_access_confirm_hook() is None
+    set_directory_access_confirm_hook(_never_called)
+    assert get_directory_access_confirm_hook() is not None
+    set_directory_access_confirm_hook(None)
+    assert get_directory_access_confirm_hook() is None
+
+
+async def test_approve_grants_session_access(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("approved").resolve()
+    calls: list[tuple[Path, AccessMode, str, float]] = []
+
+    def hook(path: Path, mode: AccessMode, reason: str, timeout: float) -> AccessDecision:
+        calls.append((path, mode, reason, timeout))
+        return AccessDecision(AccessMode.WRITE)
+
+    set_directory_access_confirm_hook(hook)
+    out = await call_async(request_directory_access, str(outside), "need the dataset", "read")
+    assert "access granted" in out
+    assert "write, session" in out
+    assert calls == [(outside, AccessMode.READ, "need the dataset", 30.0)]
+    assert session.access_grants[outside] == AccessMode.WRITE
+    target = outside / "data.txt"
+    _ = target.write_text("x", encoding="utf-8")
+    assert resolve_path(str(target), required=AccessMode.WRITE) == target
+
+
+async def test_process_grant_when_not_persisting(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("process").resolve()
+    set_directory_access_confirm_hook(lambda *_a: AccessDecision(AccessMode.READ, persist=False))
+    out = await call_async(request_directory_access, str(outside), mode="read")
+    assert "read, process" in out
+    assert session.access_grants == {}
+    assert active_workspace_policy().yolo_allow[outside] == AccessMode.READ
+
+
+async def test_deny_with_comment(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("denied").resolve()
+    set_directory_access_confirm_hook(lambda *_a: "no, that is my tax data")
+    out = await call_async(request_directory_access, str(outside))
+    assert out.startswith("error: access to")
+    assert "user comment: no, that is my tax data" in out
+    assert session.access_grants == {}
+
+
+async def test_deny_none(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("timeout").resolve()
+    set_directory_access_confirm_hook(lambda *_a: None)
+    out = await call_async(request_directory_access, str(outside))
+    assert "denied (declined or timed out" in out
+    assert session.access_grants == {}
+
+
+async def test_no_hook_denies(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("nohook").resolve()
+    set_directory_access_confirm_hook(None)
+    out = await call_async(request_directory_access, str(outside))
+    assert "no confirm hook installed" in out
+
+
+async def test_denylist_can_never_be_granted(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("secret-zone").resolve()
+    secret = outside / "secret"
+    secret.mkdir()
+    set_path_denylist(["/secret/"])
+    set_directory_access_confirm_hook(_never_called)
+    try:
+        out = await call_async(request_directory_access, str(secret), mode="read")
+        assert "can never be granted" in out
+        assert session.access_grants == {}
+    finally:
+        set_path_denylist(None)
+
+
+async def test_already_accessible_inside_workspace(
+    workspace: object,
+    session: SessionState,
+) -> None:
+    from pathlib import Path
+
+    assert isinstance(workspace, Path)
+    set_directory_access_confirm_hook(_never_called)
+    out = await call_async(request_directory_access, str(workspace), mode="read")
+    assert "already accessible" in out
+    assert session.access_grants == {}
+
+
+async def test_already_granted_skips_prompt(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("granted").resolve()
+    _ = grant_session_access(outside, AccessMode.READ)
+    set_directory_access_confirm_hook(_never_called)
+    out = await call_async(request_directory_access, str(outside), mode="read")
+    assert "already granted" in out
+
+
+async def test_invalid_mode(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace, session
+    outside = tmp_path_factory.mktemp("mode").resolve()
+    out = await call_async(request_directory_access, str(outside), mode="sudo")
+    assert "invalid mode" in out
+
+
+async def test_exec_requires_directory(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace, session
+    outside = tmp_path_factory.mktemp("exec-file").resolve()
+    target = outside / "f.txt"
+    _ = target.write_text("x", encoding="utf-8")
+    out = await call_async(request_directory_access, str(target), mode="exec")
+    assert "exec access requires a directory" in out
+
+
+async def test_missing_path(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace, session
+    missing = tmp_path_factory.mktemp("missing").resolve() / "nope"
+    out = await call_async(request_directory_access, str(missing))
+    assert "does not exist" in out
+
+
+async def test_grant_cap(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("cap").resolve()
+    policy = active_workspace_policy()
+    for index in range(MAX_ACCESS_GRANTS):
+        policy.config_allow[outside / f"d{index}"] = AccessMode.READ
+    set_directory_access_confirm_hook(_never_called)
+    try:
+        out = await call_async(request_directory_access, str(outside))
+        assert "too many active access grants" in out
+        assert session.access_grants == {}
+    finally:
+        policy.config_allow.clear()
+
+
+def test_set_config_access_installs_and_skips(
+    workspace: object,
+    session: SessionState,
+    tmp_path_factory: pytest.TempPathFactory,
+) -> None:
+    del workspace, session
+    outside = tmp_path_factory.mktemp("config-allow").resolve()
+    target = outside / "data.txt"
+    _ = target.write_text("x", encoding="utf-8")
+    missing = outside / "missing"
+    applied, skipped = set_config_access(
+        {
+            str(outside): "read",
+            str(missing): "read",
+            str(target): "sudo",
+        }
+    )
+    assert applied == [outside]
+    assert sorted(skipped) == sorted([str(missing), str(target)])
+    assert active_workspace_policy().config_allow == {outside: AccessMode.READ}
+    assert resolve_path(str(target), required=AccessMode.READ) == target
+    with pytest.raises(WorkspaceError, match="escapes"):
+        _ = resolve_path(str(target), required=AccessMode.WRITE)

tests/test_tools/test_catalog.py

@@ -4,8 +4,9 @@ from __future__ import annotations
 
 import inspect
 
-from plyngent.agent import ToolTag, tool
+from plyngent.agent import ToolRegistry, ToolTag, tool
 from plyngent.tools import default_tool_definitions, register_builtin_tools
+from plyngent.tools.access import ACCESS_TOOLS
 from plyngent.tools.catalog import ToolCatalog, ToolSource, catalog_scope, get_catalog, registration_source
 from plyngent.tools.chat import CHAT_TOOLS
 from plyngent.tools.file import FILE_TOOLS
@@ -18,7 +19,7 @@ from plyngent.tools.vcs import VCS_TOOLS
 def test_default_tool_names_match_group_lists() -> None:
     register_builtin_tools()
     selected = default_tool_definitions(surface="local")
-    groups = [*FILE_TOOLS, *PROCESS_TOOLS, *VCS_TOOLS, *CHAT_TOOLS, *TODO_TOOLS, *NET_TOOLS]
+    groups = [*ACCESS_TOOLS, *FILE_TOOLS, *PROCESS_TOOLS, *VCS_TOOLS, *CHAT_TOOLS, *TODO_TOOLS, *NET_TOOLS]
     assert sorted(t.name for t in selected) == sorted(t.name for t in groups)
     assert len(selected) == len(groups)
 
@@ -42,6 +43,45 @@ def test_public_surface_is_subset() -> None:
     assert "read_file" not in public
 
 
+def test_read_only_classification() -> None:
+    """READ_ONLY marks exactly the non-mutating builtins."""
+    register_builtin_tools()
+    read_only = {t.name for t in default_tool_definitions(surface="local") if t.tags & ToolTag.READ_ONLY}
+    assert read_only == {
+        "read_file",
+        "get_truncated",
+        "glob_paths",
+        "grep_files",
+        "listdir",
+        "tree",
+        "todo_list",
+        "wait",
+        "ask_user_line",
+        "ask_user_choice",
+        "ask_user_form",
+        "vcs_kind",
+        "vcs_status",
+        "vcs_diff",
+        "vcs_log",
+        "vcs_branch",
+        "fetch",
+    }
+
+
+def test_registry_clone_read_only_only() -> None:
+    """clone(read_only_only=True) keeps only READ_ONLY tools, nothing else."""
+    register_builtin_tools()
+    full = ToolRegistry(default_tool_definitions(surface="local"))
+    ro = full.clone(read_only_only=True)
+    assert 0 < len(ro) < len(full)
+    assert {t.name for t in ro.definitions()} == {t.name for t in full.definitions() if t.tags & ToolTag.READ_ONLY}
+    assert all(t.tags & ToolTag.READ_ONLY for t in ro.definitions())
+    assert "run_argv" not in ro
+    assert "edit_replace" not in ro
+    # Plain clone keeps every tool.
+    assert len(full.clone()) == len(full)
+
+
 def test_catalog_scope_empty_isolates_registration() -> None:
     with catalog_scope(empty=True) as catalog:
 

tests/test_tools/test_chat_tools.py

@@ -144,3 +144,51 @@ async def test_wait_tool_times_out(monkeypatch) -> None:
         registry = ToolRegistry([wait])
         out = await registry.execute("wait", '{"duration": 3}')
     assert out == "waited 3s"
+
+
+async def test_wait_tool_prompt_two_lines_with_reason(monkeypatch) -> None:
+    prompts: list[str] = []
+    monkeypatch.setattr(
+        wait_module,
+        "read_line_with_timeout",
+        lambda prompt, timeout: prompts.append(prompt) or None,
+    )
+    with temporary_backend(ScriptedBackend([])):
+        registry = ToolRegistry([wait])
+        out = await registry.execute("wait", '{"duration": 5, "reason": "tests are slow"}')
+    assert out == "waited 5s"
+    assert prompts == ["Waiting for 5s (tests are slow). Press Enter to disturb.\nReason (optional): "]
+
+
+async def test_wait_tool_prompt_two_lines_no_reason(monkeypatch) -> None:
+    prompts: list[str] = []
+    monkeypatch.setattr(
+        wait_module,
+        "read_line_with_timeout",
+        lambda prompt, timeout: prompts.append(prompt) or None,
+    )
+    with temporary_backend(ScriptedBackend([])):
+        registry = ToolRegistry([wait])
+        out = await registry.execute("wait", '{"duration": 5}')
+    assert out == "waited 5s"
+    assert prompts == ["Waiting for 5s. Press Enter to disturb.\nReason (optional): "]
+
+
+def test_wait_prompt_plain_when_not_a_tty() -> None:
+    """Prompt styling is stripped when stdout is not a TTY (pytest capture)."""
+    prompt = wait_module._wait_prompt(5, reason="tests")
+    assert "\x1b[" not in prompt
+    assert prompt == "Waiting for 5s (tests). Press Enter to disturb.\nReason (optional): "
+
+
+def test_wait_prompt_colored_on_tty(monkeypatch) -> None:
+    """On a TTY the prompt is styled: cyan status, yellow input prompt."""
+
+    class _FakeStdout:
+        def isatty(self) -> bool:
+            return True
+
+    monkeypatch.setattr(wait_module.sys, "stdout", _FakeStdout())
+    prompt = wait_module._wait_prompt(5, reason="tests")
+    assert "\x1b[36m" in prompt  # cyan status
+    assert "\x1b[33m" in prompt  # yellow input prompt

tests/test_tools/test_edit_lineno.py

@@ -19,9 +19,38 @@ def test_edit_lineno_replace_middle(workspace: object) -> None:
     _ = _read_lineno("a.txt")
     out = call_sync(edit_lineno, "a.txt", 2, 3, "TWO\nTHREE\n")
     assert "replaced lines 2-3" in out
+    assert "first: 'two'" in out  # old-content excerpt for self-correction
     assert call_sync(read_file, "a.txt") == "L1-4\none\nTWO\nTHREE\nfour\n"
 
 
+def test_edit_lineno_read_truncated_marks_only_displayed_lines(workspace: object) -> None:
+    """A max_chars-truncated numbered read must not mark the unseen tail."""
+    del workspace
+    _ = call_sync(write_file, "t.txt", "".join(f"line {i}\n" for i in range(1, 101)))
+    # Displayed complete lines are editable...
+    _ = reset_lineno_tracker()
+    _ = call_sync(read_file, "t.txt", with_lineno=True, max_chars=80)
+    out = call_sync(edit_lineno, "t.txt", 5, 5, "FIVE\n")
+    assert "replaced lines 5-5" in out
+    # ...but the truncated tail (never shown) stays unread.
+    _ = reset_lineno_tracker()
+    _ = call_sync(read_file, "t.txt", with_lineno=True, max_chars=80)
+    out = call_sync(edit_lineno, "t.txt", 90, 90, "X\n")
+    assert "not read" in out and "90" in out
+
+
+def test_edit_lineno_error_shows_read_window(workspace: object) -> None:
+    """The unread error names the read window so the model can re-read precisely."""
+    del workspace
+    _ = call_sync(write_file, "j.txt", "a\nb\nc\nd\n")
+    _ = reset_lineno_tracker()
+    _ = call_sync(read_file, "j.txt", offset=1, limit=2, with_lineno=True)  # lines 2-3
+    out = call_sync(edit_lineno, "j.txt", 1, 1, "X\n")
+    assert "not read" in out
+    assert "read lines 2-3" in out
+    assert "margin" in out
+
+
 def test_edit_lineno_requires_all_lines_read(workspace: object) -> None:
     del workspace
     _ = call_sync(write_file, "r.txt", "a\nb\nc\nd\ne\n")
@@ -37,6 +66,16 @@ def test_edit_lineno_requires_all_lines_read(workspace: object) -> None:
     assert "replaced lines 2-3" in out
 
 
+def test_edit_lineno_append_to_empty_file(workspace: object) -> None:
+    """An empty file has nothing to clobber, so appending needs no read."""
+    del workspace
+    _ = call_sync(write_file, "empty.txt", "")
+    _ = reset_lineno_tracker()
+    out = call_sync(edit_lineno, "empty.txt", 1, 1, "first\n")
+    assert "appended" in out
+    assert call_sync(read_file, "empty.txt") == "L1-1\nfirst\n"
+
+
 def test_edit_lineno_append_requires_last_line_read(workspace: object) -> None:
     del workspace
     _ = call_sync(write_file, "ap.txt", "a\nb\nc\n")
@@ -92,7 +131,7 @@ def test_edit_lineno_requires_rerun_after_write(workspace: object) -> None:
     _ = _read_lineno("f.txt")
     _ = call_sync(write_file, "f.txt", "changed\n")
     out = call_sync(edit_lineno, "f.txt", 1, 1, "x\n")
-    assert "not read" in out
+    assert "changed" in out and "re-read" in out
 
 
 def test_edit_lineno_requires_rerun_after_edit_replace(workspace: object) -> None:
@@ -101,7 +140,7 @@ def test_edit_lineno_requires_rerun_after_edit_replace(workspace: object) -> Non
     _ = _read_lineno("g.txt")
     _ = call_sync(edit_replace, "g.txt", "two", "TWO")
     out = call_sync(edit_lineno, "g.txt", 2, 2, "x\n")
-    assert "not read" in out
+    assert "changed" in out and "re-read" in out
 
 
 def test_edit_lineno_invalidates_after_successful_edit(workspace: object) -> None:
@@ -111,4 +150,19 @@ def test_edit_lineno_invalidates_after_successful_edit(workspace: object) -> Non
     _ = call_sync(edit_lineno, "h.txt", 2, 2, "B\n")
     # After the edit, line numbers are stale — must re-read before editing again.
     out = call_sync(edit_lineno, "h.txt", 2, 2, "C\n")
-    assert "not read" in out
+    assert "changed" in out and "re-read" in out
+
+
+def test_edit_lineno_detects_external_change(workspace: object) -> None:
+    """A mutation outside the file tools (run_argv, another process) is caught."""
+    import os
+    import time
+
+    assert isinstance(workspace, Path)
+    _ = call_sync(write_file, "i.txt", "one\ntwo\nthree\n")
+    _ = _read_lineno("i.txt")
+    # Simulate an external/process-tool mutation: rewrite content + new mtime.
+    _ = call_sync(write_file, "i.txt", "one\ntwo\nthree\nCHANGED\n")
+    os.utime(workspace / "i.txt", (time.time() + 1, time.time() + 1))
+    out = call_sync(edit_lineno, "i.txt", 1, 1, "x\n")
+    assert "changed since it was read" in out

tests/test_tools/test_fetch.py

@@ -8,6 +8,7 @@ from typing import TYPE_CHECKING, override
 
 import pytest
 
+from plyngent.tools.context import read_only_context
 from plyngent.tools.danger import classify_danger
 from plyngent.tools.net import fetch, grant_private_host
 from plyngent.tools.net.policy import (
@@ -199,6 +200,23 @@ async def test_fetch_get_post_put_delete(workspace: Path, http_server: str) -> N
     assert "status=204" in out_del
 
 
+async def test_fetch_read_only_context_blocks_non_get(workspace: Path, http_server: str) -> None:
+    """In a read-only context fetch only allows GET; outside it POST works."""
+    del workspace
+    port = int(http_server.rsplit(":", 1)[1])
+    grant_private_host("127.0.0.1", port)
+
+    with read_only_context():
+        out = await call_async(fetch, f"{http_server}/hello")
+        assert "status=200" in out  # GET is fine in a read-only context
+        blocked = await call_async(fetch, f"{http_server}/echo", method="POST", body="hi")
+        assert blocked.startswith("error:")
+        assert "GET" in blocked
+
+    out_post = await call_async(fetch, f"{http_server}/echo", method="POST", body="hi")
+    assert "POST:hi" in out_post
+
+
 async def test_fetch_user_agent_passthrough(workspace: Path, http_server: str) -> None:
     del workspace
     port = int(http_server.rsplit(":", 1)[1])

tests/test_tools/test_file.py

@@ -74,6 +74,7 @@ def test_edit_replace_first_only(workspace: object) -> None:
     assert call_sync(read_file, "t.txt") == "L1-1\nbb aa"
     assert "1 of 2" in result or "1 of 2 matches" in result
     assert "remain" in result
+    assert "'aa' → 'bb'" in result  # old→new excerpt for self-correction
 
 
 def test_edit_replace_max_replaces(workspace: object) -> None:

tests/test_tools/test_get_truncated.py

@@ -44,6 +44,40 @@ async def test_get_truncated_file_chains_without_gap(workspace: Path) -> None:
     assert total_read == 1000
 
 
+async def test_get_truncated_numbered_continues_and_marks(workspace: Path) -> None:
+    """A numbered read's token resumes the numbered view, gap-free and editable."""
+    from plyngent.agent import reset_lineno_tracker
+    from plyngent.tools.file import edit_lineno, read_file
+
+    (workspace / "big.txt").write_text("".join(f"line {i}\n" for i in range(1, 101)), encoding="utf-8")
+    reset_lineno_tracker()
+    first = await call_async(read_file, "big.txt", with_lineno=True, max_chars=120)
+    token = _extract_token(first)
+    assert token is not None
+    parsed = decode_truncate_token(token)
+    assert parsed is not None
+    assert parsed.kind == "file"
+    assert parsed.numbered is True
+    # The token points at the raw start of the next line (no skip, no overlap).
+    body = first.split("\n[Truncated", 1)[0]
+    shown = body.count("\n")
+    expected_raw = sum(len(f"line {i}\n") for i in range(1, shown + 1))
+    assert parsed.offset == expected_raw
+
+    # Continuation is numbered and starts right after the displayed lines.
+    cont = await call_async(get_truncated, token, max_chars=200)
+    numbered = [ln for ln in cont.splitlines() if "|" in ln and ln.strip().split("|", 1)[0].strip().isdigit()]
+    assert numbered
+    first_num = int(numbered[0].split("|", 1)[0].strip())
+    assert first_num == shown + 1
+
+    # Resumed lines are editable via edit_lineno; unseen lines stay unread.
+    out = await call_async(edit_lineno, "big.txt", first_num, first_num, "EDITED\n")
+    assert "replaced lines" in out
+    out2 = await call_async(edit_lineno, "big.txt", 90, 90, "X\n")
+    assert "not read" in out2
+
+
 async def test_get_truncated_file_missing(workspace: Path) -> None:
     token = encode_truncate_token(TruncateToken(kind="file", location="nope.txt", offset=0, limit=200))
     out = await call_async(get_truncated, token, max_chars=200)

tests/test_tools/test_mcp_tools.py

@@ -0,0 +1,93 @@
+"""MCP tool registration: namespacing, tags, catalog source, purge, handlers."""
+
+from __future__ import annotations
+
+import pytest
+
+from plyngent.agent.tools import ToolTag
+from plyngent.runtime.mcp_client import McpTool
+from plyngent.tools.catalog import catalog_scope
+from plyngent.tools.mcp import mcp_tool_name, purge_mcp_tools, register_mcp_server_tools
+
+
+class _StubManager:
+    """Duck-typed McpManager stand-in (records calls, returns canned text)."""
+
+    def __init__(self) -> None:
+        self.calls: list[tuple[str, str, dict[str, object]]] = []
+
+    async def call(self, server: str, tool: str, arguments: dict[str, object]) -> str:
+        self.calls.append((server, tool, arguments))
+        return f"{server}:{tool}:{arguments.get('text', '')}"
+
+
+def _tools() -> list[McpTool]:
+    return [
+        McpTool(
+            name="echo",
+            description="Echo text.",
+            input_schema={"type": "object", "properties": {"text": {"type": "string"}}},
+        ),
+        McpTool(name="", description="skipped: empty name", input_schema={}),
+    ]
+
+
+def test_mcp_tool_name_sanitizes_and_namespaces() -> None:
+    assert mcp_tool_name("my server", "a/b c") == "mcp__my_server__a_b_c"
+    assert mcp_tool_name("x", "y").startswith("mcp__")
+
+
+def test_register_names_tags_source_and_purge() -> None:
+    manager = _StubManager()
+    with catalog_scope(empty=True):
+        names = register_mcp_server_tools("docs", _tools(), manager=manager)  # type: ignore[arg-type]
+        assert names == ["mcp__docs__echo"]
+
+        from plyngent.tools.catalog import get_catalog
+
+        entry = get_catalog().get("mcp__docs__echo")
+        assert entry is not None
+        assert entry.source.kind == "mcp"
+        assert entry.source.plugin_id == "docs"
+        assert str(entry.source) == "mcp:docs"
+        definition = entry.definition
+        assert definition.tags == ToolTag.LOCAL
+        assert definition.description.startswith("[mcp:docs]")
+        assert definition.parameters["type"] == "object"
+        assert "text" in definition.parameters["properties"]
+
+        assert purge_mcp_tools() == 1
+        assert get_catalog().get("mcp__docs__echo") is None
+        assert purge_mcp_tools() == 0
+
+
+def test_register_read_only_flag() -> None:
+    manager = _StubManager()
+    with catalog_scope(empty=True):
+        register_mcp_server_tools("docs", _tools()[:1], manager=manager, read_only=True)  # type: ignore[arg-type]
+        from plyngent.tools.catalog import get_catalog
+
+        entry = get_catalog().get("mcp__docs__echo")
+        assert entry is not None
+        assert entry.definition.tags == ToolTag.LOCAL | ToolTag.READ_ONLY
+
+
+def test_duplicate_registration_collides() -> None:
+    manager = _StubManager()
+    with catalog_scope(empty=True):
+        register_mcp_server_tools("docs", _tools()[:1], manager=manager)  # type: ignore[arg-type]
+        with pytest.raises(ValueError, match="collision"):
+            register_mcp_server_tools("docs", _tools()[:1], manager=manager)  # type: ignore[arg-type]
+
+
+async def test_handler_proxies_to_manager_call() -> None:
+    manager = _StubManager()
+    with catalog_scope(empty=True):
+        register_mcp_server_tools("docs", _tools()[:1], manager=manager)  # type: ignore[arg-type]
+        from plyngent.tools.catalog import get_catalog
+
+        entry = get_catalog().get("mcp__docs__echo")
+        assert entry is not None
+        result = await entry.definition.handler(text="hi")  # type: ignore[union-attr]
+        assert result == "docs:echo:hi"
+        assert manager.calls == [("docs", "echo", {"text": "hi"})]

tests/test_tools/test_tree.py

@@ -67,7 +67,60 @@ def test_tree_origin_subdir(workspace: object) -> None:
     assert isinstance(workspace, Path)
     _build_sample(workspace)
     out = call_sync(tree, "src")
+    assert out.startswith("- ")
+    assert "- nested/" in out
+    assert "main.py" in out
+    assert "deep.txt" in out
+
+
+def test_tree_default_is_markdown(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    _build_sample(workspace)
+    out = call_sync(tree, ".")
+    assert out.startswith("- ")
+    assert "- src/" in out
+    assert "├──" not in out
+
+
+def test_tree_markdown_format(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    _build_sample(workspace)
+    out = call_sync(tree, ".", format="markdown", max_depth=3, max_entries=10)
+    assert "- src/" in out
+    # nested bullets are indented by 2 spaces per level
+    assert "  - main.py" in out
+    assert "  - nested/" in out
+    assert "    - deep.txt" in out
+    assert "more entries not shown" in out
+
+
+def test_tree_flat_format(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    _build_sample(workspace)
+    out = call_sync(tree, ".", format="flat", max_entries=200)
+    assert "src/" in out  # dirs keep a trailing slash
+    assert "src/main.py" in out
+    assert "src/nested/deep.txt" in out
+    assert "a.txt" in out
+    assert "- " not in out
+    assert "├──" not in out
+
+
+def test_tree_flat_total_cap(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    _build_sample(workspace)
+    out = call_sync(tree, "pkg", format="flat", max_depth=2, max_entries=10)
+    paths = [line for line in out.splitlines() if not line.startswith("…")]
+    assert len(paths) == 10
+    assert "more paths not shown" in out
+
+
+def test_tree_decorated_format(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    _build_sample(workspace)
+    out = call_sync(tree, "src", format="decorated")
     assert out.startswith("src/")
+    assert "├──" in out
     assert "main.py" in out
     assert "deep.txt" in out
 

tests/test_tools/test_workspace.py

@@ -3,13 +3,18 @@ from __future__ import annotations
 import pytest
 
 from plyngent.tools import (
+    AccessMode,
     WorkspaceError,
+    active_workspace_policy,
     check_command_allowed,
     get_workspace_root,
+    mode_covers,
+    parse_access_mode,
     resolve_path,
     set_command_denylist,
     set_path_denylist,
 )
+from plyngent.tools.context import SessionState, bind_session
 
 
 def test_resolve_relative_and_absolute(workspace: object) -> None:
@@ -27,6 +32,89 @@ def test_escape_rejected(workspace: object) -> None:
         _ = resolve_path("../outside")
 
 
+def test_escape_error_hints_request_tool(workspace: object) -> None:
+    del workspace
+    with pytest.raises(WorkspaceError, match="request_directory_access"):
+        _ = resolve_path("../outside")
+
+
+def test_access_mode_parse_and_covers() -> None:
+    assert parse_access_mode(" Read ") is AccessMode.READ
+    assert parse_access_mode("EXEC") is AccessMode.EXEC
+    assert parse_access_mode("bogus") is None
+    assert mode_covers(AccessMode.EXEC, AccessMode.WRITE)
+    assert mode_covers(AccessMode.WRITE, AccessMode.WRITE)
+    assert not mode_covers(AccessMode.READ, AccessMode.WRITE)
+
+
+def test_config_grant_modes(workspace: object, tmp_path_factory: pytest.TempPathFactory) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("granted")
+    target = outside / "data.txt"
+    _ = target.write_text("x", encoding="utf-8")
+    policy = active_workspace_policy()
+    policy.config_allow[outside] = AccessMode.READ
+    try:
+        assert resolve_path(str(target), required=AccessMode.READ) == target
+        with pytest.raises(WorkspaceError, match="escapes"):
+            _ = resolve_path(str(target), required=AccessMode.WRITE)
+        policy.config_allow[outside] = AccessMode.WRITE
+        assert resolve_path(str(target), required=AccessMode.WRITE) == target
+        with pytest.raises(WorkspaceError, match="escapes"):
+            _ = resolve_path(str(target), required=AccessMode.EXEC)
+    finally:
+        policy.config_allow.clear()
+
+
+def test_session_grant_covers_subtree(workspace: object, tmp_path_factory: pytest.TempPathFactory) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("session")
+    nested = outside / "a" / "b"
+    nested.mkdir(parents=True)
+    with bind_session(SessionState(access_grants={outside: AccessMode.EXEC})):
+        assert resolve_path(str(nested), required=AccessMode.EXEC) == nested
+    with pytest.raises(WorkspaceError, match="escapes"):
+        _ = resolve_path(str(nested), required=AccessMode.READ)
+
+
+def test_file_grant_is_exact_path(workspace: object, tmp_path_factory: pytest.TempPathFactory) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("file-grant")
+    granted = outside / "one.txt"
+    sibling = outside / "two.txt"
+    _ = granted.write_text("1", encoding="utf-8")
+    _ = sibling.write_text("2", encoding="utf-8")
+    policy = active_workspace_policy()
+    policy.config_allow[granted] = AccessMode.READ
+    try:
+        assert resolve_path(str(granted), required=AccessMode.READ) == granted
+        with pytest.raises(WorkspaceError, match="escapes"):
+            _ = resolve_path(str(sibling), required=AccessMode.READ)
+        # A file grant does not cover its parent directory.
+        with pytest.raises(WorkspaceError, match="escapes"):
+            _ = resolve_path(str(outside), required=AccessMode.READ)
+    finally:
+        policy.config_allow.clear()
+
+
+def test_denylist_wins_over_grant(workspace: object, tmp_path_factory: pytest.TempPathFactory) -> None:
+    del workspace
+    outside = tmp_path_factory.mktemp("denied")
+    secret = outside / "secret"
+    secret.mkdir()
+    key = secret / "key"
+    _ = key.write_text("k", encoding="utf-8")
+    policy = active_workspace_policy()
+    policy.config_allow[outside] = AccessMode.WRITE
+    set_path_denylist(["/secret/"])
+    try:
+        with pytest.raises(WorkspaceError, match="matched '/secret/'"):
+            _ = resolve_path(str(key), required=AccessMode.READ)
+    finally:
+        set_path_denylist(None)
+        policy.config_allow.clear()
+
+
 def test_path_denylist(workspace: object) -> None:
     from pathlib import Path