fix(mcp): auto-detect project via roots/list when no rootUri (#196)

[colbymchenry]

Problem

MCP tools failed with CodeGraph not initialized even when the index existed, reported in #196 by @zhangyu1197.

When a client launches the MCP server from a directory other than the project and doesn't pass a rootUri/workspaceFolders in initialize (some IDE/JetBrains-family integrations), the server fell back to its own process.cwd(), missed the project's .codegraph/, and returned a misleading "Run 'codegraph init' first" on every call. The only workaround was passing projectPath to each tool by hand.

Root cause: rootUri/workspaceFolders are LSP-style fields (non-standard for MCP) — the spec's actual mechanism for a client to expose its workspace root, roots/list, was never implemented.

Fix

• transport.ts — the stdio transport can now send server→client requests and match their responses by id. Previously a roots/list reply would have been dropped as "Invalid Request" (responses carry no method). Includes a timeout so a non-answering client degrades gracefully, and pending requests are rejected on shutdown.
• index.ts — when initialize carries no explicit path, the server no longer commits to cwd. On the first tool call it asks the client via roots/list (gated on the roots capability), uses the first root, and only falls back to cwd if that yields nothing. One-shot guarded so it never re-issues roots/list per call. The fast-initialize contract from MCP server fails to connect with Claude Code: Content-Length framing vs newline-delimited JSON transport mismatch #172 is preserved — resolution stays lazy and off the handshake path.
• tools.ts — the "not initialized" error is now actionable: it names the directory it searched and tells you to pass projectPath or add --path /abs/project, instead of pointing at a re-init you don't need.

Tests

New __tests__/mcp-roots.test.ts (3 tests, real spawned server over stdio):

• resolves the project from roots/list when no rootUri is sent
• returns the actionable error when there's no signal and no roots capability
• still honors an explicit rootUri without asking for roots

Full suite green (639 passed), including the #172 handshake-timing regression test.

Credit to @zhangyu1197 for discovering and diagnosing the issue, and for the projectPath workaround.

Closes #196

🤖 Generated with Claude Code