Currently, upon installation, the jbpm definitions will not go into jcr but stay in the file system. When loading workflows values from jcr are considered but will always be replaced by the ones from the filesystem. Both should be changed - much like it's implemented in 4.5. Like that users:

• would be able to use e.g. the jpbm Eclipse plugin to modify their flow files but still have it bootstrapped into jcr
• directly adapt flows in jcr without having to fiddle around with the file system