Directories listed in allowed_directories in ~/.copilot/permissions-config.json do not suppress the "path outside your allowed directory list" prompt for shell commands.

Describe the bug

Directories listed in allowed_directories in ~/.copilot/permissions-config.json do not suppress the "path outside your allowed directory list" prompt for shell commands. /add-dir with the identical path fixes it for the session.

Startup log says it loaded:
[INFO] permissions::api_orchestrator] Applied persisted allowed directories {"count":2,"location_key":"..."} 
Probable cause: in app.js, addAdditionalDirectory() is only called inside the paths.add handler. hydrate_location_permission_directories applies persisted dirs to the native permission service but never performs that sync, so the path gate used for shell commands doesn't see them.
Secondary: the prompt's "Yes, and add these directories to the allowed list" option maps to {kind:"approve-for-session"} — the wording implies persistence it doesn't have.

Affected version

GitHub Copilot CLI 1.0.79.

Steps to reproduce the behavior

Repro: add an absolute dir to allowed_directories under a location key; start a session whose git root is that key; run a shell command reading a file under that dir → prompt appears. Run /add-dir  → no more prompts.

Expected behavior

No response

Additional context

No response

Start in app.js, comparing addAdditionalDirectory() in the paths.add handler with hydrate_location_permission_directories and the persisted-directory startup path. Reproduce with an absolute allowed_directories entry, then run a shell command reading a file under it. Done means persisted directories suppress the path prompt like /add-dir, and the prompt wording accurately reflects session-only approval.