`ConfigStore.reload()` re-parsed every section except `[skills]`, so
`/model --persist` and any other in-place reload kept serving the skill config
the process started with — including `[skills].enabled`, which is what decides
whether the skill tools exist at all.
Skills are discovered from user-level directories by default: an explicit
``paths`` list wins, then the built-in sources (our own user config dir, and
other harnesses' skill dirs) with the project-scope dirs behind their own
switch. A name found twice shadows the lower-priority copy without hiding it.
``inject_catalog`` / ``max_catalog_skills`` bound what reaches the system
prompt, ``enabled = false`` registers nothing, and ``allow_write`` is the
standing grant for editing skills (default: ask every time). A malformed
section degrades to the defaults, like [agent] and [mcp].
NCBM