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answers:

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I want to track the workspace of eclipse by source control so that important settings can be backed up. However, there are a lot of kind of *.index inside the .metadata folder of workspace. Some information are important, for example Mylyn repository, but some information is merely cached files and thus, doesn't make sense to me for being tracked.

In short, what files inside eclipse workspace that should be tracked so that I can restore the working workspace after problems (like meta data file deleted, etc.)

A: 

You should not track metadata by source control. Project settings are in .classpath,.settings and .project files/folders. Metadata folder holds only eclipse settings, local tasks, caches and indexes.

Ha
Isn't that .mylyn data stored inside workspace metadata are precious data to be tracked?
Phương Nguyễn
You can always redownload it (except private notes) from your bug tracker.
Ha