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MPLAB packaging versus building and excluding files or directories


I would think this would be obvious, but the documentation doesn't go into much detail.
We develop MPLAB projects for the PIC32 under FreeRTOS using the xc32-gcc compiler.
All of our projects follow a specific directory structure and use relative paths, so I would like to exclude the FreeRTOS header and source files when packaging the project, but obviously not when building the project. My question is how best to do this.
I believe that the reference design that I used as a starting point created logical folders for the FreeRTOS source and then added specific files as existing sources, because they get included in the zip archive and also appear under "General" category of the "Project Properties" dialog box, as well as the "File Inclusion/Exclusion" category.
I suspect what I need to do is remove these logical folders from the project and then modify the gcc command line to specify the necessary include directories.
Does that sound correct?

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