Passing in a PWMOut still works but is deprecated. It will be
removed in CircuitPython 8.0.0
This also switches STM32 timer indices and channel indices to
0-based in our pin data rather than `- 1` everywhere. The latter is
more bug prone.
Most of the way for #3264
Tested on Metro M0, Metro M4, Feather S2, Feather nRF52840, Feather
STM32F4 and Arduino RP2040.
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 introduces the new macro SAM_D5X_E5X. This is mostly the same
as SAMD51 before, except in a few places where a special case for
SAME54 is required
Its slimmed down by removing the qstr and bit packing TCC info.
The trinket m0 build actually grows by 20 bytes. The arduino zero
build shrinks by 188 bytes.
