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Test case: 1. Place some sources under VCS. 2. Create empty project. 3. Create some logical folder. 4. Add sources to this logical folder. 5. Change one of the files -> the logical folder will not be annotated.
The idea of the fix can be borrowed from NetBeans modules projects. The Important Files is a logical folder, but it is annotated if some it's child files is changed.
Will be back to this bug in next release, Now it looks like some "mix: of Disk and Logical folders should be implemented.