Always process modules/packages given with -m/-p - #2786

Manually tested. There are currently no tests for -m and -p, and I don't care enough to add new infrastructure for this. (The existing usage of cmd: mypy -m blahblah in many tests is different -- it does not actually use the -m command line flag but resolves the modules to paths in the test framework.)

Whoops, this closes #2778, not #2779.