Fix pull, merge and start from non-TLDs

Pull #45 (f11ff4c) only fixed this for feature/hotfix switch. These
changes are needed any time git-submodule is run.

Also check for submodule updates in feature-merge.
Remove unneeded submodule init
Consolidate submodule functions and combine commands
Merge pull request #50 from iFixit/fix-hotfix-feature-from-anywhere

Fix pull, merge and start from non-TLDs