cmd: Use git cli to add report files, rather than repo.index.add

It seems that the GitPython repo index add method tries to do additional permission fiddling that the CLI does not, and that doesn't work with our shared repos. Hopefully this will help fix some of the permission issues we've been running into.

assigned to @joseph-betzwieser

I've checked this out and confirm it works for me, on a report generated by Vlad. We should go ahead and merge.

approved this merge request

enabled an automatic merge when all merge checks for cf4d7780 pass

canceled the automatic merge

mentioned in commit 61715db5

merged