Recently switched to handling version control outside of eclipse and now whenever I return to the project and do something that triggers a project refresh (changing the credentials or selecting file system refresh from the project menu)  the auto-build generates 100s of "File only saved locally, not to server" for system files (i.e. .DS_Store and .git files).  Is there anyway to exclude these from the auto-build?

Screenshot:
![enter image description here][1]


  [1]: https://i.sstatic.net/dPiV5.png