glob files are miscomputed when the bug file does not share a common root with the rest of the project

[JasonGross]

When the file being minimized shares no common root with the rest of the project, coq_makefile incorrectly adds -R . Top to the end of the list of arguments, overriding everything before it. See https://github.com/coq/coq/issues/7845. This is a bug in Coq, I believe, but we should probably work around it somehow. Maybe by doing the default root calculation ourselves and preemptively adding -Q at the beginning.