I'm sure you had situations when Eclipse was behaving strange. Probably your first attempt is to clean and refresh the project. Sometimes it's not enough, but luckily there is a "brute force" method:
1) Delete project from workspace (don't delete it from filesystem)
2) Delete .settings, .project and .classpath and target (assuming that you use Maven)
3) Import project into workspace
There you go. Fresh checkout is another option, but does not work very well if you have uncommitted changes.
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