Add testcase for bug 394497 (ignore-modules/include-dependencies).

This adds a testcase that would fail without the bugfix for bug 394497
and now passes.

This did require undoing some of the changes to generateModuleList but
the only real behavior change (beside merging duplicate ignored module
checks) was to move the step that generates module dependencies to occur
earlier so that it can happen before the filter steps

CCBUG:394497