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This is actually part #2 of issue #98662. For example, if you open Apache Ant sources as an automatic project, profile some unit test, and save a snapshot of results, the project will be marked modified because you create an unignorable nbproject/private/profiler/configurations.xml. For this project type, there is *no* designated directory for IDE-generated stuff inside the project directory; if you need a place to put files it will have to be inside the user directory, or in a user-selected location. (You can use e.g. ProjectUtils.getPreferences if you want to store project-specific information.) Similarly for Maven projects I would assume, when profiling is implemented for them.
Profiler in maintenance - not for 6.8 (significant changes required).
I think I already fixed this. *** This issue has been marked as a duplicate of 159642 ***