Moved git submodule init/update to git pull in dev-helper

dev-helper and dev-installer should not do anything unless told to.
Moved git submodule stuff to the git-pull function.
linktool displays branching previous links

refs #5235

Some links have multiple parents (ie. links that point to them). Updated
display of previous links to show the hierarchy, using indents.  Also
updated insertbefore to work with multiple parents.