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With bug 356620, JDT/Core is providing the support to specify the index files when the class path library is specified. PDE container should locate the index files and should specify when the classpath libraries are specified.
I have put in the high level approach, the implementation with the bug and some questions. Please let us know if this is inline with what you would need.
Per https://bugs.eclipse.org/bugs/show_bug.cgi?id=356620#c37, JDT/Core support for this feature retargetted to early M5.
We will only add this if we have a concrete request.