* I deleted the molgenis_apps I was running , because after some point , when I was trying to run it , eclipse was crashing!
* I downloaded a fresh copy of molgenis_apps. 
* I tried to run ..didn't work, so I started adding jars available in lib folder in both molgenis and molgenis_apps. 
* I downloaded and added some jars (the ones that I commited and broke the build), later removed from svn by Joeri/
* Currently I am getting an error in molgenis JpaDatabase.java, that does not go away (!) but at least both of my apps are running (ONLY) in standalone , NOT in tomcat . I am trying to set up in new server this configuration with the standalone but I am getting an error of missing xpath:  /home/antonakd/bbmri/molgenis_apps/build_common.xml:212: java.lang.NoClassDefFoundError: com.sun.org.apache.xpath.internal.XPathAPI