Description

During CI-682 live testing, the file watcher infrastructure was confirmed working (non-bare mode), but fire_hooks is never called when directory changes or file changes are detected. Despite a [hooks] section in the TOML config, hooks_config.cwd_changed appears to be empty at runtime.

Reproduction Steps

1. Add [hooks] section to testing.toml with cwd_changed and file_changed entries
2. Run: cargo run --features full -- --config .local/config/testing.toml
3. Change working directory or modify a tracked file during session
4. Observe: working directory changed is logged, but no hook fires

Expected Behavior

• hooks_config.cwd_changed should contain the hook command from TOML
• fire_hooks should be called with the CwdChanged event

Actual Behavior

• working directory changed log entry appears (watcher is running)
• fire_hooks is NOT called — hooks_config.cwd_changed appears empty despite TOML config
• Possible TOML nested-key parse issue OR hooks firing but output not captured

Environment

• Version: HEAD a0f1a76
• Features: full
• Mode: non-bare CLI session

Logs / Evidence

From CI-682 live test:

• file change watcher started — confirmed (non-bare mode)
• working directory changed — confirmed
• hooks_config.cwd_changed appears empty at hook-dispatch time
• with_hooks_config is skipped in --bare mode (runner.rs:2153) — not the issue here

Notes

• file_changed hook: watcher starts but FileChanged events not received in test window (may be timing)
• Both issues may share root cause in TOML config deserialization of the [hooks] section