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.
if you are a regular eclipse user than you might have got this error many times. the error simply says, “you’ve made changes in files in your workspace from outside eclipse”. the simplest solution would be to select the project and press f5 (right click -> refresh).
if you need more explanation you can read from this web site
i was not able to resolve this error by either refresh or by turning on "native polling" workspace feature. turned out my project was also opened in two instances of eclipse. once i closed the other instance, the error went away. so make sure your project is only opened at one place if you are seeing this error.
if this occurs trying to delete a folder (on *nix) and refresh does not help, open a terminal and look for a symlink below the folder you are trying to delete and remove this manually. this solved my issues.
a little hint. the message often appears during rename operation. the quick workaround for me is pressing
ctrl-y (redo shortcut) after message confirmation. it works only if the renaming affects a single file.
when you open an eclipse workspace from within a clearcase view and try to rename the project, you will often get the pop-up warning ... “resource ‘project’ is out of sync with the file system”. if refreshing the project does not fix the problem, then do the following workaround: a. open workspace without being in a view b. select the project in project explorer c. clearcase -> associate project (project should now look like project  ) d. right click project -> refresh (vob sub-folders should now be empty) e. right click project -> rename ... f. enter new name
now you can close the workspace, reopen it in a view and refresh the project. you may also dissociate the project if you prefer the project not to be associated with the vob.
this happens to me all the time.
go to the error log, find the exception, and open a few levels until you can see something more like a root cause. does it says "resource is out of sync with the file system" ?
when renaming packages, of course, eclipse has to move files around in the file system. apparently what happens is that it later discovers that something it thinks it needs to clean up has been renamed, can't find it, throws an exception.
there are a couple of things you might try. first, go to window: preferences, workspace, and enable "refresh automatically". in theory this should fix the problem, but for me, it didn't.
second, if you are doing a large refactoring with subpackages, do the subpackages one at a time, from the bottom up, and explicitly refresh with the file system after each subpackage is renamed.
third, just ignore the error: when the error dialog comes up, click abort to preserve the partial change, instead of rolling it back. try it again, and again, and you may find you can get through the entire operation using multiple retries.
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.
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.
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