I develop Java code with Eclipse and regularly get this message:
resource is out of sync with the filesystem.
Right-click > Refr
For the new Indigo version, the Preferences change to "Refresh on access", and with a detail explanation : Automatically refresh external workspace changes on access via the workspace.
As “resource is out of sync with the filesystem” this problem happens when I use external workspace, so after I select this option, problem solved.