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Well I think I have things figured out, but please correct me if I'm wrong, Glassfish is like a Tomcat a server/container for java EE applications I don't know about JBoos but I'm guessing its the same, so as I already configured Tomcat, and most web servers I know use Tomcat I think I'm going to pass on installing Glassfish, I do however have a copy of the J2EE jars in my PC so I'm going to use them for programing.
My Mac has the javac file so I figure out it has the JDK or the file wouldn't be there so an other question answered.
Finally I found out that the differences between bashrc and bash.profile its that bashrc runs each time you open a bash, and bash.profile runs each time you open a session on the Mac so, either of the two files works for setting the path, and as I already configured the mysql path on the bashrc I'm going to stick with it although now that I'm not installing glassfish, setting the JAVA_HOME path is not necessary I'm going to set it just in case.
Thank you all, hope this helps some day.