fix: refresh shared indexer after knowledge base updates

[Helweg]

Summary

Refresh the shared tool indexer immediately after knowledge base config changes so in-session indexing and search use the updated configuration without requiring another restart.

Changes

• rebuild the shared Indexer from parsed config after add_knowledge_base updates the project config
• rebuild the shared Indexer after remove_knowledge_base so the in-memory tool state stays in sync
• add a regression test covering both add/remove refresh behavior in tests/tools-knowledge-bases.test.ts

Testing

How were these changes tested?

• Unit tests added/updated
• Manual testing performed
• Build passes (npm run build)
• Typecheck passes (npm run typecheck)
• Tests pass (npm run test:run)
• Lint passes (npm run lint)

Release Labels

• Added at least one release category label (feature, bug, performance, documentation, dependencies, refactor, test, chore, or skip-changelog)
• Added at most one semver label (semver:major, semver:minor, semver:patch) when needed

Related Issues

N/A