Mypy merges errors from files with similar names

[msherry]

Given the following directory structure,

.
├── pkg1
│   └── controller.py
└── pkg2
    └── controller.py

flycheck-pycheckers will merge mypy output for the two files named controller.py. Newer versions of mypy have started reporting output for all files involved, and the mypy lint runner, although it attempts to filter them out, doesn't do this correctly. This is exacerbated by the fact that the data dictionary received in fixup_data sometimes contains a full filepath, and sometimes just the filename, within the same run of mypy.