After discussing with danh, I noticed that `a/**/b` would not match `a/b`.
After correcting this and re-running "pre-commit run --all", additional
files were reindented, including the codeformat script itself.
In #4683, tannewt noticed that uncrustify was not running on some
file in common-hal.
I investigated and found that it was not being run on a bunch of paths.
Rather than make incremental changes, I rewrote list_files to work
bsaed on regular expressions; these regular expressions are created from
the same git-style glob patterns.
I spot-checked some specific filenames after this change, and all looks good:
```
$ python3 tools/codeformat.py -v --dry-run tests/basics/int_small.py ports/raspberrypi/common-hal/pulseio/PulseIn.c extmod/virtpin.c tests/thread/thread_exit1.py ports/raspberrypi/background.h extmod/re1.5/recursiveloop.c
tools/codeformat.py -v --dry-run tests/basics/int_small.py ports/raspberrypi/common-hal/pulseio/PulseIn.c extmod/virtpin.c tests/thread/thread_exit1.py ports/raspberrypi/background.h extmod/re1.5/recursiveloop.c
uncrustify -c /home/jepler/src/circuitpython/tools/uncrustify.cfg -lC --no-backup extmod/virtpin.c ports/raspberrypi/background.h ports/raspberrypi/common-hal/pulseio/PulseIn.c
black --fast --line-length=99 -v tests/thread/thread_exit1.py
```
recursiveloop and int_small are excluded, while PulseIn, virtpin,
and background are included.
Testing running from a subdirectory (not _specifically_ supported though):
```
(cd ports && python3 ../tools/codeformat.py -v --dry-run raspberrypi/common-hal/pulseio/PulseIn.c ../extmod/virtpin.c)
../tools/codeformat.py -v --dry-run raspberrypi/common-hal/pulseio/PulseIn.c ../extmod/virtpin.c
uncrustify -c /home/jepler/src/circuitpython/tools/uncrustify.cfg -lC --no-backup ../extmod/virtpin.c raspberrypi/common-hal/pulseio/PulseIn.
```
As a side-effect, a bunch more files are re-formatted now. :-P
