Application in apps dir are some times not loaded at startup

If I deploy the itests using the command line deployment tool, stop the server and restart it. The itests application is not loaded in the new server.

My guess is this is cause by the deployment identification code. When the deployment tool installs an application, it unpacks it directly into the apps dir. When the server restarts, the startup code does not know what kind of module the unpacked directory is since it can not see the file extension of the original archive.