Carrying a complete copy of Scintilla would bloat the repository size and might get relevant over time.
Do you know and tried the already existing update script (https://github.com/geany/geany/blob/master/scripts/update-scintilla.sh)?
It also just works on an extract tarball and copies relevant files and patches our changes in.

I don't argue against the git-subtree solution, it sounds pretty good actually.
I'm just concerned about the repository size and duplicating efforts which have already been done in the above mentioned script.

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