Hi Remi,
a simple test is to try out your project if it still builds/works with all the ignored files and folder ignored.
/FLASH: yes, this is the output folder as 'debug' in my case. That folder name depends on your project settings.
/MQXLITE: I think this is generated from the MQXLite Processor Expert component, so you can ignore this one.
Debugger settings: they are created at project time, but not aftewards. Do not ignore them.
Dito for Startup code, do not ignore them.
Linker file: that depends if you generate them from Processor Expert or not. If yes, then you can ignore the linker file, otherwise not.
I hope this helps,
Erich