I thought we are trending towards using upstream as-is, with only small changes needed (including new files).

Yes, we are, but currently it's only the ctags/main directory (there's the 6-line diff but I want to eliminate it as well - will do it in a separate pull request once this pull request is merged). But for ctags/parsers it's more like ~10000 LOC diff and for many parsers it will be a bi-directional process - we have some code that should be added upstream and some upstream code should be added to our parsers. I think in the current situation git subtree wouldn't be very practical.

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