[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2019-09-30T17:41:23Z"
 content="""
It may be that git is not overwriting the file with its new content, but is
unlinking it and then writing the new content. If so, that could explain
the assistant's behavior, since it could notice the file has been deleted,
and might commit that before it notices it's been added back.

I tried stracing git checkout, and it indeed does unlink
a modified file then it opens the file for write and writes out the new
content. Kind of surprising it's not more atomic.

The nature of the assistant is that it's never going to be guaranteed to
always make commits that make logical sense in the same way that manually
committing will. It might be possible to improve this by having it delay
committing removals for some period of time.
"""]]
