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
After this change, the following program works for me on the MIMXRT1010-EVK:
```python
import pwmio
import board
p = pwmio.PWMOut(board.D13, frequency=1_000_000, variable_frequency=True)
p.duty_cycle = 32868
while True:
pass
```
Querying and varying the duty_cycle and frequency work as well.
The lowest frequency obtainable is about 2kHz; there is an additional
divider which would allow lower PWM frequencies (I think 1kHz is important
for servos?)
Something odd happens with very low duty cycles, such as
```python
>>> p.frequency = 2000
>>> p.duty_cycle = 2
```
instead of a symmetrical waveform, it's asymmetrical. With `duty_cycle=4`,
the effect disappears. The reason for this is probably hidden in the
datasheet, but could affect servos or other things that count pulse
widths.
