This causes a few problems. First, it prevents the JAR files from showing up under the lib directory in the tree-view.
Actually they should be locked IF they were automatically added to your build path and thus show up in your package view. This is a setting under Window > Prefs > MyEclipse > J2EE Projects > Web Projects.
Second, it prevents me from deleting the files (or the project) through the Eclipse IDE or through Windows Explorer. Third, it prevents the files from being removed from the project (or from the project’s classpath) if the nature is removed at a later time.
Eclipse will typically release the lock after shutdown and after a fresh startup you can remove them. But agreed, this can be annoying if you are adding/removing JARs a lot, although most users won’t be and the indexer keeps read locks open on these JARs for autocomplete.
If I turn off build-automatically and rebuild the project at a later point none of this happens.
This could be related to automatically parsing the JAR contents, but that’s just a guess.
Also, I have tried adding this nature to a Web Tools project and this problem does not occur, which leads me to believe it is local to MyEclipse.
WTP doesn’t have the option to automatically mount JARs in the WEB-INF/lib dir into the build path, we do, that might be why you are not seeing this behavior with WTP.