fix(installer): write Claude project-local MCP config to .mcp.json (#207) (#209)

Project-local installs wrote the MCP server to ./.claude.json, which Claude Code never reads — project-scoped servers must live in .mcp.json. The codegraph tools silently never loaded until users renamed the file by hand. Local installs now write ./.mcp.json and migrate any stale ./.claude.json entry on install and uninstall (siblings preserved). Global installs (~/.claude.json, user scope) were already correct.

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

CHANGELOG.md

@@ -46,6 +46,17 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
   Thanks to [@essopsp](https://github.com/essopsp) for the repro.
 
 ### Fixed
+- **Installer (Claude Code)**: project-local installs (`Just this project`)
+  now write the MCP server to `.mcp.json` in the project root — the file
+  Claude Code actually reads for project-scoped servers. Previously they
+  wrote `.claude.json`, which Claude Code ignores, so the codegraph tools
+  silently never appeared and you had to rename the file by hand to make it
+  work. Re-running `codegraph install` (or `codegraph init`) on an affected
+  project migrates the stale `.claude.json` entry into `.mcp.json`
+  automatically; uninstall cleans up both. Global (`All projects`) installs
+  were unaffected — they correctly target `~/.claude.json`. Closes
+  [#207](https://github.com/colbymchenry/codegraph/issues/207). Thanks to
+  [@Jhsmit](https://github.com/Jhsmit) for the report and the workaround.
 - **MCP**: source-omission markers in `codegraph_explore` and
   `codegraph_context` output are now language-neutral (`... (gap) ...`,
   `... (trimmed) ...`, `... (truncated) ...`) instead of C-style `//`