## Why
`codex app-server daemon restart` previously reused saved settings without applying feature flags supplied on the command line.
## What changed
Apply `--enable`, `--disable`, and boolean `-c features.*` overrides during an explicit restart and persist them for subsequent restarts. Accept nested `enabled` values, normalize feature aliases, and replace conflicting saved aliases while preserving unrelated settings.
Reject invalid feature toggles before stopping the daemon or saving settings.
## Testing
Add integration coverage for overrides on stopped and running daemons, alias replacement, preservation of saved settings, restarts without flags, and rejection of non-toggle keys without interrupting the running daemon.
GitOrigin-RevId: 14a657bc4758b9c248e363f9dac58f8887070a04