feat(mcp): expose knowledge-base tools to all MCP clients

[dkhokhlov]

Summary

Registers add_knowledge_base, list_knowledge_bases, and remove_knowledge_base as MCP server tools so every MCP client (Codex, Claude Code, Jcode, and other MCP hosts) can manage knowledge bases.
Previously these operations were exposed only to the OpenCode plugin and the Pi extension (under host-native names); MCP clients had no way to add, list, or remove knowledge bases through the MCP
server.

Implements #298

Background

The knowledge-base operations (addKnowledgeBase, listKnowledgeBase, removeKnowledgeBase in src/tools/operations.ts) were deliberately scoped to OpenCode and Pi, not overlooked: KB management
mutates persistent per-host config and rebuilds the shared indexer, and OpenCode/Pi pass a per-call worktree so KB edits land in worktree-local config. The MCP server, however, runs at a fixed
project root (process.cwd() / --project) for its lifetime, and all existing MCP tools already operate on that fixed root. Exposing KB tools on the startup root is therefore consistent with the
existing MCP model, not a new behavior.

Changes

• src/tools/tool-names.ts — MCP_TOOL_NAMES is no longer a bare alias of PORTABLE_TOOL_NAMES; it is now PORTABLE_TOOL_NAMES + the three KB tools. PORTABLE_TOOL_NAMES is left untouched because it
  is a Pi contract (tests/pi-package.test.ts asserts Pi exposes every portable name, and Pi exposes KB tools only under its knowledge_base_* aliases).
• src/adapters/mcp/register-tools.ts — registers the three KB tools after code_communities, calling the existing operation functions with runtime.projectRoot + runtime.host. Returns are wrapped
  so a response whose text starts with "Error: " is reported with MCP isError: true; informational returns ("already configured", "not found") are not flagged as errors.
• docs/tools.md — recomputes the host surface matrix (portable core 15; MCP 18 tools + 5 prompts; OpenCode 19; Pi 18), adds codebase_edit_context and code_communities to the portable list,
  reclassifies the KB tools as shared by MCP + OpenCode, and documents the worktree, multi-host, config-layering, and repo-only-blame semantics.
• README.md — notes that MCP clients can add/list/remove knowledge bases via the exposed tools.
• tests/mcp-server.test.ts — updates the stale tool-count test name to 18.
• tests/mcp-knowledge-bases.test.ts (new) — MCP-to-operation integration tests: real temp project + MockIndexer + in-memory client; verifies add persists to the host-specific config path
  (.claude/codebase-index.json for claude, .codebase-index/config.json for codex) and refreshes the indexer; list shows Exists; remove clears it; non-existent path returns isError: true with
  "Error: Directory does not exist" and writes no config / triggers no refresh; remove of an unconfigured path returns "Knowledge base not found" without isError; missing required path is rejected
  by Zod with isError: true.

Behavior notes

• add_knowledge_base writes the path to the project-local host config of the MCP server (e.g. /.claude/codebase-index.json for the claude host, /.codebase-index/config.json for
  codex/jcode/pi) and refreshes the index. It is not a user-global change.
• The index is the union of the project code and the configured knowledge-base folders (getScopedRoots() = {projectRoot} ∪ knowledgeBases). Knowledge-base source/text files are searchable by all
  retrieval tools.
• list_knowledge_bases shows the union of project-local and user-global knowledge bases. remove_knowledge_base edits only the project-local layer, so a knowledge base inherited from a user-global
  config returns "Knowledge base not found" and is not removed.
• Git blame metadata is collected only for files in the project git repository. Knowledge-base files outside the repository remain searchable by content but have no blame, so
  blameAuthor/blameSha/blameSince filters match only in-repo files.
• The MCP server runs at a fixed project root for its lifetime; KB tools are not per-call worktree-aware. For worktree-local KB management, use OpenCode or Pi.

Tests

• npx vitest run tests/mcp-server.test.ts tests/mcp-knowledge-bases.test.ts — green.
• npx vitest run tests/pi-package.test.ts tests/tools-knowledge-bases.test.ts — Pi contract and existing operation tests unaffected.
• Full npx vitest run — green (pre-existing failures on main unchanged; none caused by this change).

Manual verification

Installed and driven over stdio with raw JSON-RPC (--project --host claude, embeddings via OLLAMA_HOST → nomic-embed-text):

1. tools/list → 18 tools, KB trio present.
2. add_knowledge_base (sibling repo json-c) → Total knowledge bases: 1, wrote project-local .claude/codebase-index.json (only knowledgeBases; no inherited provider setting leaked).
3. list_knowledge_bases → Status: Exists.
4. index_codebase → 350 files processed, 6391 new chunks embedded (union of repo + json-c).
5. Retrieval after rebuild: codebase_search "json_object_from_file" → json-c definitions with full source (json_util.c:68-98, score 0.99); implementation_lookup → authoritative def in json-c;
   codebase_peek → json-c lh_table_lookup/json_object_object_add alongside repo hits (union confirmed), with repo hits carrying git blame and json-c hits carrying none — matching the documented
   blame semantics.
6. remove_knowledge_base → Removed; list_knowledge_bases → No knowledge bases configured.

Checklist

• Exposes add_knowledge_base / list_knowledge_bases / remove_knowledge_base to all MCP clients
• Preserves the PORTABLE_TOOL_NAMES Pi contract
• Maps "Error:"-prefixed returns to MCP isError: true
• Adds MCP integration unit tests
• Updates docs and README
• Verified end-to-end on the published package, including KB-content retrieval after rebuild