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Make LibGit2Sharp aware of external changes to the index #526

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With #525 a new method ReloadFromDisk() has been added to the Index which overwrites its content with the state of the on-disk index file.

RetrieveStatus already calls this method.

This method call should be deployed to many more methods: most of the Index methods along with some other ones (Commit, Stash, Reset, ...).

Maybe the first step of this change would be to try to list all the candidates...

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