When upgrading a THREDDS Data Server (TDS), it is important to fully undeploy the running TDS before deploying the new TDS. Not doing so can cause conflicts between old and new Java classes and/or JSP pages (among other things). The reason for this is that Tomcat and other webapp containers have working directories [1] of some kind in which to keep files they need (like compiled JSP pages).
So, here is the process we follow when we upgrade the TDS on our systems (we use Tomcat, but the process should be similar for other webapp containers):
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