So.. the plot thickens. After talking with a sys admin locally he indicated that my own group changes were attempting to modify ldap defined groups, and for obvious reason, were not allowed.
So, I created a new local group, added my user and tomcat to it, switched all the files group settings around and verified that tomcat could do anything it wanted with the files, which it could. It could at least read them before, without any change, but could not write. Now there is full RWX on all target files.
I then started tomcat with great hope using the jrebel agent, and I had the same exact problem again. I am starting to think jrebel does not understand linux file paths? Or thinks the path is a partial path? I don’t have a root path or anything defined int the jrebel.properties it is referencing.