Reported by @normal wigeon
In the Codex CLI, using . (current working directory) correctly scopes MCP servers to the project's directory, with fallback cwd resolving properly. In the Codex Desktop app, MCP servers initialize at startup without re-scoping when switching projects, causing . (or relative/current dir references) to default to root / across all projects. For servers omitting an explicit directory and relying on internal cwd lookup, this makes them read the working directory as / (root).
When working in a specific project, we need to be able to forward the current project directory to a MCP server. Somehow, or reload the MCP servers again with the correct project directory
cwd is / in all projects in Codex Desktop, and not the project directory
MacBook Pro :: macOS 26.2