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Custom resource settings are indicated by overlay icon "system includes" in Project Explorer. This is misleading because any not related to include directories change in build settings will provoke overlay appearance. The overlay should rather be related to "tool settings" metaphor. Besides I join with the complainers about the icon not being esthetically pleasing like in bug 171809.
Created attachment 155054 [details] patch
Created attachment 155055 [details] new overlay icon
Committed on HEAD (CDT 6.1 aka 7.0)