Created an internal JIRA to track this issue until we get the public one running.

I don't want to require NTA_CONF_DIR for the open source project to build and work.  The nupic repo has nupic-default.xml that installs to conf/default/ and I want this to get used by default.  It doesn't make sense to have this install to conf/site/default/ hence the problem.  I am going to move forward with this change and we can revisit it once we have a chance to discuss what we want long term.