mach: update-manifest misses local changes

[gterzian]

I've noticed a few times that if you make a change to an existing test, ./mach update-manifest does nothing locally. Later, it fails on CI(example: https://tools.taskcluster.net/groups/Sl1yBFfwRP6Vh2ELmd8Hxw/tasks/CebOEynkQruZJ-A0FGfYrQ/runs/0/logs/public%2Flogs%2Flive.log#L525).

Not sure how I fixed it last time, or whether this happens intermittently, but this time I can guarantee that I tried it a few times locally, I even deleted MANIFEST.json and rebuild it, yet it was rebuild without taking into account the latest changes(0f53873#diff-684fc482ea12f526b30118a7d4cfa714R33).

[highfive]

cc @wafflespeanut

[jdm]

I'm hopeful that this has been fixed by web-platform-tests/wpt#17785.

[CYBAI]

It's been synced in https://github.com/servo/servo/pull/23767/files?file-filters%5B%5D=.py#diff-dca0930be0d5a55410bfecf0b0ab7a31 👀