AllMigrationsPluginTest.php still needs some love, just need to make sure the others tests drop all tables created.
Fixing plugin loading in tests
Fixing tests for startup and run methods.
Fixing tests for runWithFailures method.
Fixing tests for generate methods.
Fixing tests for status method.
Uncommenting and fixing remaining tests.
Removed non-used code, adding doblock for setUp method.
Making sure files will not exists if tests get interrupted.