Patch file was missing some internal folders
Added full integration tests and fixed new dir creation

  Since the full integration test is more efficient of time usage for us, I've
  added the tests that do the end-to-end functionality verification. In the
  process, I've found a bug with our code and fixed it. Applying on an already
  deployed dir is still failing which needs to be fixed.
Added deletion of in-place deleted files

  Before, when applying an in-place patch, old files were not removed which
  we now do. We still need to change this to use a non-specified target dir.
Added handling of omitted target dir on apply action

  Since we may wan an inplace patch application, assume that whenever we
  don't specify the target directory that the old directory will be also
  the target.
Change the phrasing on TODOs to be more accurate now
Merge branch 'more_testing'