feat(tools): Wave 3 - standardize all 9 non-mature tools to robust pattern

Standardize nia-read, nia-grep, nia-explore, nia-index, nia-manage-resource,
nia-context, nia-package-search, nia-auto-subscribe, nia-e2e with:
- Try-catch error handling with shared formatters
- Config checks (apiKey, feature enabled)
- Abort signal handling
- Runtime validation replacing unsafe casts
- TDD approach: failing tests first, then implementation

All 9 tools now follow the mature pattern from nia-search.ts
Tests: 39 new tests added, all passing