Fix misdetection of project root with `--stdin-filename` (#3216)

There are a number of places this behaviour could be patched, for
instance, it's quite tempting to patch it in `get_sources`. However
I believe we generally have the invariant that project root contains all
files we want to format, in which case it seems prudent to keep that
invariant.

This also improves the accuracy of the "sources to be formatted" log
message with --stdin-filename.

Fixes GH-3207.