The behavior you identify is the basic Eclipse platform workflow. If you wish to have the project classpath automatically maintained when jars are added/removed from the WEB-INF/lib folder you should consider disabling the auto-build workbench preference, see Window menu>Preferences>Workbench. As you have identified any changes to a project’s classpath results in a rebuild of the project when the “auto rebuild when resources are modified” is enabled (the default).
For large projects I typically leave the auto-build preference enabled and disable the JSP validation preference. Then I manually invoke JSP validation on a periodic basis. Also I recently entered an enhancement request to provide JSP validation of selected resources.
Michael
MyEclipse Support