This was an old bug in EGit where it automatically found the .git in your home directory and then scanned all the files in the home directory. It has been fixed in newer versions of EGit.
But you may still have the repository configured, even after you upgraded. Do the following:
- Open the Git Repositories view
- Find the repository that causes the problem
- In the context menu, select Remove Repository from View
Then restart Eclipse.
Read full article from eclipse: "re-indexing repository workspace" or "Computing Git status for repository workspace" - Stack Overflow
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