Logic updates for find_dep_app.py

closes #3397

For now we are going to look one directory up from HERD_TRUNK_DIR and the base of MOOSE's directory and traverse from there.  There are several new pieces of logic here.  First we are going to limit the search depth to speed things up.  Also we are going to ignore directories containing a file named ".ignore".

Finally there is new logic for figuring out which version of MOOSE to use.  
1) We prefer MOOSE_DIR first
2) If in trunk we prefer stable moose
3) if not in trunk we prefer github moose (not trunk)