meson: Add explicit check: kwarg to all run_command() calls

meson: Add explicit check: kwarg to all run_command() calls

This is required since Meson 0.61.0, and causes a warning to be
emitted otherwise:

https://github.com/mesonbuild/meson/commit/2c079d855ed87488bdcc6c5c06f59abdb9b85b6c
https://github.com/mesonbuild/meson/issues/9300

This exposed a bunch of places where we had broken run_command()
calls, unnecessary run_command() calls, and places where check: true
should be used.

Part-of: <https://gitlab.freedesktop.org/gstreamer/gstreamer/-/merge_requests/1507>