But I've removed that code? By relying on the coverage argument being insert before the command in the tests, it'll be treated as a global argument and get removed before shell alias code sees it. That's means that in drush itself we're down to the init code in drush_main() an extra global option and a shutdown function in order to get the coverage. The rest is the collection code in Drush_CommandTestCase, and a fix to shellAliasesCase::testShellAliasDrushRemote() which looks at the whole command line.

Anything else I've missed?