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To reproduce: create a web module and add a JSP. Execute the JSP. Delete the WEB-INF directory. It is no longer a web module but it stays deployed.
This seems to me to be quite a strange case - sounds like an enhancement. I would suggest to prevent users to delete the WEB-INF folder and web.xml file from the IDE or show a nice warning dialog, that this would lead to the webmodule became invalid. I wouldn't handle the case when the user corrupts the structure externally - after doing that the webmodule continues running until someone tries to reload it or stop s the whole server. When the server is started for the next time, there will be some error messages in the server output, but the user will be able to undeploy the corrupted webmodule via tomcat instance in server registry.
first, we do not undeploy anything now (although Ana would probably argue we should) second, the user can still undeploy from server registry
problem does not exist in trunk (WEB-INF is always a regular directory now)
Verified.