fix(watchers): debounce skills and settings reload bursts

[chioarub]

Summary

Fixes #1366.

• Debounce skills reload bursts so folder moves and renames produce one reload instead of repeated immediate reload work.
• Add a skills reload cooldown to avoid back-to-back reload cascades during multi-wave chokidar bursts.
• Remove redundant direct skill cache clearing because clearCommandsCache() already clears skill caches.
• Debounce settings filesystem fanout so bursty settings events produce one cache reset and one listener notification batch per source.
• Harden cleanup paths so pending timers and late async callbacks do not run after disposal/reset.

Why

External file operations can produce many chokidar events in a short period. Before this change, those events could repeatedly run ConfigChange hooks, invalidate caches, re-read disk, and notify React listeners, which could saturate the UI thread and make OpenClaude appear frozen.

Implementation notes

• Skills changes still pass through ConfigChange hooks before cache clearing and notification.
• Blocking ConfigChange hooks still prevent skills reloads and settings fanout.
• Skills reloads now serialize in-flight hook work and defer cache clearing if newer events arrive before hooks finish.
• Settings fanout tracks per-source generations so stale accepted changes cannot emit after newer same-source events are blocked or pending.
• Programmatic notifyChange() and MDM polling keep immediate fanout behavior; only filesystem watcher fanout is debounced.
• Regression tests use explicit dependency overrides instead of mock.module(...) so the serialized Bun suite does not leak mocks into later test files.

Testing

• GitHub Actions smoke-and-tests passed: bun run smoke, bun test --max-concurrency=1, Python tests, PR intent scan, provider tests, provider recommendation tests.
• GitHub Actions web passed: web typecheck and build.
• Local: bun test src/utils/skills src/utils/settings
• Local: bun test --max-concurrency=1 src/utils/skills/skillChangeDetector.test.ts src/utils/plugins/pluginLoader.test.ts src/utils/settings/changeDetector.test.ts src/tools/BashTool/bashPermissions.test.ts
• Local: bun run build
• Local: git diff --check

Manual validation

• Started OpenClaude with an isolated CLAUDE_CONFIG_DIR and a dummy skills/dummy-skill/SKILL.md fixture.
• Externally renamed/moved the dummy skills folder in a burst and edited SKILL.md.
• Confirmed the skills burst produced one ConfigChange:skills hook/reload in the debug log.
• Confirmed the TUI remained responsive after watcher bursts by sending input and receiving the normal Ctrl-C exit prompt.
• Repeated with a settings file change/delete-recreate burst and confirmed one Settings changed from userSettings app-state update in the debug log.