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Pass subcommand as a regular param, which allows passing git parameters
like -c before it. This was already done in the pipeing set of functions,
but not the command running set.
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To avoid old versions of git-annex getting confused.
There is no upgrade required though.
We switch back to 3 when going from direct to indirect.
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This avoids some small overhead by only running the check once per command;
it also ensures that, even if the command doesn't find anything to run on,
it still fails to run when in a bare repo.
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Handles our file right, but not theirs.
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Automatic merge resoltion code needs to be fixed to preserve objects from
direct mode files.
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Joey Hess