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Git detects .classpath as local changes and will not allow a "pull" “pull” while these changes are present in your working folder. One way to get around this is to stash the local changes, do the pull, then pop the stash. There is another way, however, that will not stress out Eclipse with a re-index.
By default, Git uses a bit in git metadata to determine if a file has changed. This is much more efficient than actually comparing the contents of the file.
The command...command…
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git update-index --assume-unchanged {myClassPathFile}
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... … will reset that bit so that it looks like the file is unchanged. So if you issue this command for each classpath file you should never have to stash them again.
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Note that this setting will "stick" “stick” until turned off manually, or until you re-clone the repository. So don't don’t use it on files you have changed but don't don’t want to commit yet, unless you are prepared to manually set the bit afterword.
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When you're ready to submit code with a Pull Request, create a Jira case and use the case number in your commit messages, e.g. "[JIRA-1234] adding new functionality". When submitted update the Jira case with a link to the pull request on GitHub.
Advanced Topics
Advanced Git Topics - Preferred workflow, get yourself out of git trouble, and other cool stuff