backport relevant mypy 0.990 fixes from main

backport relevant mypy 0.990 fixes from main

Changes from ebb54e80a5a52d0cce4cba1abc21c707a42c2c73
which are relevant here.

Adjusted the test suite which tests the Mypy plugin to accommodate for
changes in Mypy 0.990 regarding how it handles message output, which affect
how sys.path is interpreted when determining if notes and errors should be
printed for particular files. The change broke the test suite as the files
within the test directory itself no longer produced messaging when run
under the mypy API.

Change-Id: I1728fd3bd21a4d499db0a4939ee27c67b2c34123