updates to support sumaclust svn co

This merge includes the following additions:

(1) The Sumaclust Makefile exists in a subdirectory of the checked out repository, a new option called "make-folderpath-relative-to-local" is added to application.py which states this subdirectory and forces compilation to occur within it.

(2) It can happen at times that an 'svn co' will require command-line user interface to accept a certificate by typing one of the letters (R)eject, accept (t)emporarily or accept (p)ermanently. Although newer svn versions (1.6 and up) can pass the options "--non-interactive --trust-server-cert" to overcome this issue, it does not always work. For this, I've also included an echo statement (echo t | svn co ... ) in the svn_checkout() method to temporarily accept a certificate without any command interface. 
Sorry, please disregard, saw your note in the other qiime-deploy-conf pull request