Presently, MyEclipse expects JSPs to reside under a Web Project’s <web-root> folder. This is to enable a simple deployment model based on an exploded WAR. JSPs that reside elsewhere will not be available for deployment, hot-swap update, or debugging. We have an open request to enhance this to a user configurable policy. I don’t have an exact ETA on when this will be relaxed but I do know it is very very sooooooon!