In the source code of Workflow designer delivered with the source code of JIRA is missing the following files:
rw-rr- 1 yilinmo staff 10076 Aug 13 10:33 swfobject-min.js
rw-rr- 1 yilinmo staff 1106671 Aug 13 10:33 jira-workflow-designer-flex-2.6.13.swf
rw-rr- 1 yilinmo staff 1256 Aug 13 10:33 jwd-min.js
Which are delivered with the standalone version and war version of JIRA.
As consequence, the workflow designer plugin is not working correctly after the JIRA is built.