Summary

• New MCP tools update and embed so an agent can re-index collections and generate vector embeddings without shelling out to the CLI.
• update accepts optional collection (scope to one) and runUpdateCommand (opt-in git pull etc.); failing update_command marks that collection skipped and continues.
• embed is incremental by default; opt-in force: true wipes and regenerates all vectors.
• buildInstructions updated: existing qmd embed CLI hints replaced with tool-style Call the \embed` tool` plus a new "Maintenance:" tool list.

Implementation notes

• Both handlers reuse the existing pure-logic functions reindexCollection and generateEmbeddings from src/store.ts via store.internal.
• Synchronous return only, no MCP progressNotification — the agent flow is short by design.
• EmbedResult.docsProcessed is mapped to docsEmbedded at the tool boundary so the public MCP shape is stable independent of the internal field name.
• runShellCommand (private helper) executes the YAML-configured update_command via sh -c. Documented as trusted-source-only.

Test plan

• npx vitest run test/mcp.test.ts — 65/65 passing.
• Manual end-to-end through Claude Code (qmd-feat MCP server registered locally):
  • tools/list shows update and embed alongside existing tools.
  • update with no args re-indexed myrag (2 new, 5 updated, 454 unchanged, 5 orphaned cleaned, 133ms; surfaced needsEmbedding: 7).
  • embed with no args embedded the 7 pending docs (120 chunks, 0 errors, 14.2s, force=false).
• Reviewer: spot-check runShellCommand security note (src/mcp/server.ts, JSDoc above the helper) — confirm the trusted-source-only wording is acceptable.
• Reviewer: confirm field-name mapping docsProcessed → docsEmbedded is acceptable as the public MCP shape.

🤖 Generated with Claude Code