core/tools: mark only displayed lines read on truncated read_file

read_file(with_lineno=true) marked the whole requested slice before
applying the max_chars cap, so a truncated read silently unlocked every
line of the file for edit_lineno even though the model never saw them.
Mark only the complete numbered lines actually returned (excluding the
[Truncated] marker); the unseen tail stays unread.

src/plyngent/tools/file/read.py

@@ -83,14 +83,10 @@ async def read_file(
     if start >= len(lines):
         return ""
     slice_lines = lines[start:end]
-    if with_lineno:
+    body = _format_with_lineno(slice_lines, start_lineno=start + 1) if with_lineno else "".join(slice_lines)
-        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)
     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 +98,21 @@ 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")
+        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}"

tests/test_tools/test_edit_lineno.py

@@ -22,6 +22,22 @@ def test_edit_lineno_replace_middle(workspace: object) -> None:
     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_requires_all_lines_read(workspace: object) -> None:
     del workspace
     _ = call_sync(write_file, "r.txt", "a\nb\nc\nd\ne\n")