Add --safe-reference for repo init

[GoogleCodeExporter]

If you use --reference, then get rid of the referenced project tree, all 
projects based on this will no longer clone properly.

I propose adding a new option to do a "one time reference" to speed up the 
initial clone, then repack afterwards so the new project tree no longer relies 
on the referenced project tree. 

A new subcommand should also be added to "repair" a project tree that has 
previously used --reference. 

The command to repack is `git repack -ad`, and to remove the reference is `rm 
.git/objects/info/alternates`. 



Note: can someone change this in to a feature request please? It doesn't give 
me the option to.

Original issue reported on code.google.com by [email protected] on 21 Feb 2015 at 12:49