Function run_mcp_stdio 

pub fn run_mcp_stdio(
    db: SharedDb,
    db_dir: Option<PathBuf>,
    reader: impl BufRead,
    writer: impl Write,
) -> Result<()>

Run the MCP loop until reader hits EOF.

db_dir is where the store lives on disk. mushroomdb mcp <db> passes it; a caller that has only a handle passes None, and the one tool that needs a path — sync, which re-runs this binary against the store — reports that it cannot run rather than guessing one.