Adding a clean target which does not use find

Also revamping the clobber target's find command so that it omits
directories properly.  I wanted there to be only one complicated find
command in our Makefiles for cleaning temporary files instead of
three, this patch achieves that goal.

Refs #4061, #4068.
cleaned up warnings (refs #4024)
Merge pull request #4078 from jwpeterson/clean_no_find

Adding a clean target which does not use find
Merge pull request #4080 from aeslaughter/contrib

cleaned up warnings
Added test with non-unique material propery names. #4081
#4081 Fixed the input file so dm3 is active.