fix(mcp): auto-detect project via roots/list when no rootUri (#196) (#214)

MCP tools failed with "CodeGraph not initialized" when a client launched
the server outside the project and sent no rootUri/workspaceFolders — the
server fell back to its own cwd, missed the project's .codegraph/, and
returned a misleading "run codegraph init" error on every call. The only
workaround was passing projectPath by hand to each tool.

When no explicit path is given, the server now asks the client for its
workspace root via the standard MCP roots/list request (gated on the
client advertising the roots capability) before falling back to cwd. This
required teaching the stdio transport to send server->client requests and
match their responses by id (previously responses were dropped as invalid).

When a project still can't be resolved, the error now names the directory
it searched and tells the user to pass projectPath or add --path to the
MCP config, instead of pointing at a re-init they don't need.

Reported-by: @zhangyu1197
Closes #196

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -57,6 +57,23 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
   Thanks to [@essopsp](https://github.com/essopsp) for the repro.
 
 ### Fixed
+- **MCP**: tools no longer fail with "CodeGraph not initialized" when the index
+  actually exists. This hit clients that launch the MCP server from a directory
+  other than your project and don't report a workspace root in `initialize`
+  (some IDE/JetBrains-family integrations) — the server fell back to its own
+  working directory, missed the project's `.codegraph/`, and returned the
+  misleading "Run 'codegraph init' first" on every call. The only workaround
+  was passing `projectPath` to each tool by hand. Now, when no project path is
+  supplied, the server asks the client for its workspace root via the standard
+  MCP `roots/list` request (when the client advertises the `roots` capability)
+  before falling back to the working directory — so detection just works for
+  spec-compliant clients. When it still can't resolve a project, the error is
+  now actionable: it names the directory it searched and tells you to pass
+  `projectPath` or add `--path /abs/project` to the server's MCP config args,
+  instead of pointing you at a re-init you don't need. Closes
+  [#196](https://github.com/colbymchenry/codegraph/issues/196). Thanks to
+  [@zhangyu1197](https://github.com/zhangyu1197) for the report and the
+  `projectPath` workaround.
 - **MCP**: the server no longer hangs on startup under WSL2 when the project
   lives on an NTFS `/mnt/*` mount. Setting up the recursive file watcher
   there took tens of seconds — every directory read crosses the Windows/9p