JarPackageFragmentRoot.computeChildren very slow in reference search

For a project with a lot of libraries on the classpath searching the workspace for references of a certain class takes several minutes to complete.

After profiling a reference search `JarPackageFragmentRoot.computeChildren` seems to be the hot spot, see screenshot.
Executing the same search again is not running faster so it seems there is no index/caching involved. Quite a bit of object allocation as well.

Eclipse version: 2024-12

Start by locating JarPackageFragmentRoot.computeChildren and profiling a reference search in a project with many classpath libraries, as described in the issue. Compare repeated searches and allocation behavior; done means the reference search no longer spends most of its time in this method and repeated searches show the investigated caching or indexing behavior.

Written by the indexing model from the issue text.