Debug within custom project structure

[xxxrs]

Hi all,

I am wondering how it is possible to debug my MCX application on my Freedom board with on board debugger (LinkServer), but using a custom project structure, which differs from the code-generation folder structure.

Background: we are developing our software in strict software layer architecture to make MCUs exchangeable. Therefore all Driver code is put to one directory, consequentially some intermediate layers and the application are located in other folders.

Now after adapting the make file(s) I am building a bin file, which I want to flash using LinkServer after according setting. 

The result is the error message: "'Launching xxx LinkServer Default' has encountered a problem. Error with command: arn-none-eabi-gdb --version".

When creating a test project within MCUXpresso with default folder structure, there are no issues downloading the program and starting a debug session. (that's why I assume that it has to do with the changed project structure)

What can I do? How do others handle their own project structures and what needs to be taken care of?

Thanks and BR