[blainemotsinger]

Summary

Fixes the stale-index gap reported in #36: query_knowledge was served from an index built once at startup, so store edits made outside write_knowledge/update_knowledge (hand edits, git checkout, migration scripts) were visible to list_knowledge but silently absent from query_knowledge.

Changes

• search.Index records a store fingerprint (per-ref source file path, size, mtime) at build time. Query re-checks it and, when files changed, builds a fresh in-memory index and swaps it in atomically, closing the old one after in-flight queries drain. Deleted entries disappear because the replacement index is built from scratch (bleve has no Delete path here).
• Unchanged stores take a fast path without the rebuild lock; rebuilds are serialized separately from query access.
• New reindex_knowledge MCP tool forces a full rebuild.
• Org-level knowledge now indexes every top-level *.md under .agents/knowledge/ (shared knowledge.OrgKnowledgeFiles) instead of the architecture.md/review.md allowlist, in both the query index and the Grep/Glob augment hook.
• README updated for auto-refresh, the new tool, and the org *.md behavior. Project store entries refreshed (sub-001, new dec-005).

Verification

• gofmt -l . clean
• go vet ./... clean
• go build ./... clean
• go test ./... 9/9 packages
• go test ./search/ -race -count=10 clean
• make eval-mock 18/18 PASS

Closes #36