Remove metadata.json and update application readme.
Remove metadata.json and update application readme.

* Metadata.json can be generated with the rake tasks.
* Use 'metadata[cookbook]' and 'metadata_all' to generate .json.
* Application readme needed a few more clarification points.

RobertNorthard/java,cellux/java,cookbooks/mc-java,RobertNorthard/java,foreflight/java,broadinstitute/java,udayas81/JAVA,cookbooks/oc-java,cposture/java,cookbooks/hw-java,Nikhil424/chef-repo,juliandunn/java,bgandon/java,cposture/java,gsaslis/java,RobertNorthard/java,Nikhil424/chef-repo,cellux/java,dcode/java,bitmonk/chef-java,gosquared/java,mrb/java,GannettDigital/chef-java,cellux/java,GannettDigital/chef-java,juliandunn/java,bitmonk/chef-java,gosquared/java,cposture/java,bgandon/java,udayas81/JAVA,Nikhil424/chef-repo,foreflight/java,LateRoomsGroup/java,gsaslis/java,bgandon/java,bitmonk/chef-java,LateRoomsGroup/java,dcode/java,mrb/java,gsaslis/java,dcode/java,nshemonsky/chef-java,nshemonsky/chef-java,GannettDigital/chef-java,Nikhil424/chef-repo,nshemonsky/chef-java,broadinstitute/java,foreflight/java,LateRoomsGroup/java,mrb/java,zenoss/java,juliandunn/java