Avoiding "resource is out of sync with the filesystem"

Window -> Preferences -> General -> Workspace

Just right click on the file or on the project and click Refresh. The error will vanish. I also faced the same issue and it worked for me.

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.

You can enable this in Window - Preferences - General - Workspace - Refresh Automatically (called Refresh using native hooks or polling in newer builds)

The only reason I can think why this isn't enabled by default is performance related.

For example, refreshing source folders automatically might trigger a build of the workspace. Perhaps some people want more control over this.

There is also an article on the Eclipse site regarding auto refresh.

Basically, there is no external trigger that notifies Eclipse of files changed outside the workspace. Rather a background thread is used by Eclipse to monitor file changes that can possibly lead to performance issues with large workspaces.