798 JSPs == ~1200 seconds (1.5 seconds per) == 20mins average
Even if you double that to 3 seconds a page (is this what you observe if you validate a page?) is still 40 mins, less than the “over and hour” estimate you gave… I wonder if you are running into memory issues? Do you give ME plenty of ram? (256?)
And yes heavy use of libs does cost in compile time. The compile process is the Jasper2 compiler run over the JSP page to make a servlet Java file, then javac run on the Java file. We can look into speeding this up in the future by moving back to using the JDT compiler, but aparently its a pretty serious PIA to get the compiling environment setup correctly for the JDT compiler to run so we are using javac for now. It is an open enhancment.
Also IIRC Jasper2 isn’t the fastest compiler on earth… and just the plain fact that your project is huge. You shouldn’t need to rebuild it more than once a week at most I imagine as MyEclipse supports hot deploy you should only be needing icremental builds mostly.