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After performing a "Build All" by right clicking a folder in the explorer, a display update occurs which marks all java nodes as dirty (the "10101" binary icon). Once the build completes successfully, the files are still marked as dirty until you right click on them, when the flag is cleared.
I don't know exactly where this issue belongs, so guessing and passing to java module. Please reassign further if I'm wrong.
I can no longer reproduce this. Please reopen and provide more accurate steps to reproduce if it happens again.