Early on when working with WebSphere, I made the mistake (out of frustration and other momentary elements) of removing applications by force, simply deleting them from the server’s directory structure.
Ever since, the beast that is WebSphere was angry: no matter what I tried, it kept attempting to load the missing applications. Finally, I seem to have found the place where the application references were hiding:
cells\ENYZHLNode01Cell\nodes\ENYZHLNode01\serverindex.xml is the file that among other things, tells WebSphere which applications to load. In short, remove the missing applications from it, and you get a nicer, cleaner startup from WebSphere.
