Tomcat should NEVER load the jars inside "/lucee-server/bundles", to avoid this we have moved the "lucee-server" directory out of the lib folder. So if Tomcat is loading this jars you need to change the classpath defintion to avoid this at any coast!
We even plan to make a warning in the admin overview page if this is happening.
Lucee normally should remove all jars used by an extension and no other extension is using when uninstalled, BUT if this jars are also loaded by tomcat it is possible (specially under windows) that Lucee is not able to remove this jars because they are blocked by tomcat.
Jars inside "/lucee-server/bundles" are loaded only on demand, so if the core and no extension is using them, they are not loaded, you can see which jars are loaded in the admin under info/bundles.
can you raise a ticket about cfhttp-cachedwithin, we will check.
we plan the possibility to customize a lucee bundle online, but like i said in a proper installation uninstalling an extension should be no problem, but we will run some tests. what OS are you using?
Micha