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20131204-1205f74381c7. Seems to be a recent regression in dev builds, or at least I do not remember seeing it until this build. After Team > Commit, the Projects tab and the edited file are still marked with a blue badge, as if still modified. (‘git status -s’ from a shell confirms that they are not.) The badges do eventually go away, but it seems to take a couple of minutes, whereas previously it was essentially immediate. (Even on a small repository with maybe a couple dozen files.)
Yeah, i played and fixed a P4 (http://hg.netbeans.org/main-golden/rev/53eeedd59d99) and forgot to implement a relevant method (http://hg.netbeans.org/main-golden/file/f8460a42fb0d/git/src/org/netbeans/modules/git/FileStatusCache.java#l149). I noticed after an hour and fixed it immediately but unfortunately the fix got stuck somewhere along the way and has not made it into a dev build yet. The fix: http://hg.netbeans.org/main-silver/rev/da05cf580d1b
Please reopen if you can still get this in later dev builds.
Fine in 20131206-3422eed6fdbf.