Revert "About to revert the entire universe. Please stand by."

This reverts commit f73f3029d776ee1e25b64221c9230ae0e752809b.
Revert "The allele manager is now in Ruby."

This reverts commit 4814b016b85fe8e2e5a43d1c94256cd1ee8c7a82.
Revert "Refactoring package names."

This reverts commit 0ec227c8c0ed757e7b9ecccf9fe062aa5d7b3392.