Upon startup, MIEngine sets the debugger working directory to the location of the debugged program executable (See LaunchLocalDebuggerCommand() in src/MICore/UnixUtilities.cs).
Later, if neither the "processId" or "customLaunchSetupCommands" options are set, then the debugger working directory is set to the path held in the "cwd"/WorkingDirectory launch option. If "processId" or "customLaunchSetupCommands" is set, the debugger working directory remains as that of the debugged program executable. See GetInitializeCommands() in src/MIDebugEngine/Engine.impl/DebuggedProcess.cs
I believe that the path held in "cwd" should be applied as the debugger working directory in all cases - for consistency and because documentation does not say that this option is sometimes ignored