Fix multiple path manifest and manual bug

Hi !

As agreed the fix based on Henrik Martinsson. I could not merge his modifications causes the fork linking is broken, so i put the modifications into a commit directly for this PR.

So, this fix is an improvement of mine 8b0f5c0842426c38eafc73e809695ff2257dd084.

If you want to merge it, you can close #60 after merge :)