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Adjust behaviour on missing commits & moved repository

@thorstenkampe reported #376 (closed) about confusing behaviour when setting git.intree in an existing repository. This was caused by three underlying issues:

  1. The documentation on git.intree only said that you should set it when cloning, but neglected to clarify what would happen if it was set in a preexisting repository.
  2. The error message was technically correct, but not terribly helpful.
  3. And as an aside, creating a new Git repository with existing commits known to hg-git is most likely an error. But I'm not entirely certain that it's always an error, so we'll just go with a warning for now. At least that provides informs the user of what happened.

Fixes #376 (closed)

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