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
This fixes some missing and incorrectly-assigned pins for the SparkFun Thing Plus RP2040 protoboard so that they actually match what the board says. This also changes the default SPI pins from the SD card pins to the breakout pins on the side of the board.
Added board definition for the Sparkfun MicroMod RP2040.
Mostly followed the format for pins from the MicroMod nRF52840 board
definition, as MicroMod tries to standardize pins across
microcontrollers.
