Watch custom scan paths for filesystem changes

[Railly]

Context

scanAll() scans every path in settings.customScanPaths, including the current vault, but getWatchPaths() only includes built-in tool directories and project-home discovery. Changes under custom roots therefore remain stale until a manual refresh or restart.

Evidence:

• src/scanner.ts:344-349 scans custom paths.
• src/scanner.ts:366-390 omits custom paths from watcher discovery.
• src/main.ts:46-52 adds the vault as a custom path.

Task

Include existing supported skill directories below every custom scan root in the watcher set. Normalize and deduplicate the resulting paths.

Acceptance criteria

• Changes below custom scan roots trigger refreshes.
• Behavior works when project scanning is disabled.
• Duplicate paths do not create duplicate watchers.
• Tests cover addition, modification, and deletion under a custom root.