Bug 897559 - Use |repo manifest| to parse manifest

This is easier to maintain and parses some elements that were being
ignored like "remove-project".

Also no longer accept a manifest file parameter. Always use the root
workspace's current manifest.
Revert "Bug 890065 - Add a flag for optionally disabling sources.xml"

This reverts commit 36900c6306ac6950191ddc7cb5d5b813d3649d11.