This should not be configurable, instead this should be considered a major blocking bug and be fixed asap.
I have just began evaluating the possibility of using this IDE when I stumbled across this thread here and I can confirm that it will indeed put absolute paths into this file. This would cause all kinds of problems as soon any of my team members would checkout an existing project from the repository on his machine containing absolute paths that were once valid on a different machine but might not even exist anymore.
You guys from Freescale/NXP know what version control is and how software is built nowadays and what developers actually want and need, don't you? I hope you do.
This is a show stopper bug, I cannot even think about using this IDE until this is fixed.