Preserve shared bundled skill caches

[copyberry]

Preserve shared bundled skill caches

Why

The bundled system-skill cache is shared by every process using the same
CODEX_HOME. A service with bundled skills disabled must not remove cache
files that another service still uses.

What changed

• Filter system skill roots from disabled services without deleting the shared
  cache.
• Ensure bundled system skills are installed during loads when they are
  enabled, including after a runtime configuration change.

Testing

Add app-server coverage for preserving the cache across enabled and disabled
services and refreshing stale cached skills after runtime enablement.

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