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With debug messages enabled, "incorrect order" will be output whenever a commit is processed before its parents have been processed. This can be determined by checking to see if a parent isn't mapped to a new commit, but it has been processed.
Please read git-subtree.txt for documentation. Please don't contact me using github mail; it's slow, ugly, and worst of all, redundant. Email me instead at apenwarr@gmail.com and I'll be happy to help. Avery