I will add that Eclipse requires that it's view of the local file system stay in sync, if you are constantly running out-of-process tasks that are changing anything on the file system you will always get these issues. However there are two things you can do to fix this, 1 is to turn on the automatic refreshing, that is under Window > Prefs > General > Workspace. The second is (I believe) a setting for Ant scripts that you can tell it to refresh the workspace after execution. Both of these will help avoid the problem you are having.
- Refresh
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