Adding skip-mode functionality to initialize

The initialize.py script used to halt on any git-error. This pull request adds the skip-mode functionality wherein user can provide an option to the script to skip the git-errors and continue with the checking-out of the repos.
Resolves issue #1 
Add a comment here that mentions the expected content/format of this file.  It would be nice if I had some idea of its contents before I got to the code that parses this configuration file.

I opted to go look at a specific example: https://github.com/SeattleTestbed/softwareupdater/blob/master/scripts/config_initialize.txt

The second item after the git repository appears to be a directory.  It is probably worth mentioning in the document/comment here.