meson: check the return value of run_command

By default, errors are not checked and a command that is somehow broken will just capture incorrect output (likely an empty string). Current development versions of meson now raise a warning for this implicit behavior, and advise explicitly setting the check: kwarg to determine whether a failing return code should be considered an error.

Since none of the commands in this project are expected to fail, mark them as required to succeed.

In the process of this fix, also fix commands that fail when they shouldn't, so that they succeed.