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ClassIndex.codebaseIndexes map is not cleared. I played a little bit with the IDE and experienced, that method JMManager.disposeCodebase() is never called. This method is only one which removes elements from map (more precisely called static method ClassIndex.removeIndex()). The caller of disposeCodebase() method - cleanUpCodebases() - is called, but I did not understood enough the logic to fix it.
Steps to reproduce: i) start IDE, ii) open some project(s), iii) close all projects, iv) open another project(s), v) again you can close projects. Steps ii) to v) can be repeated. The number of items in ClassIndex.codebaseIndexes is still growing.
As I explained in issue 46550 we clean codebases only if there are no references to the corresponding classpath elements. The fact that the codebases are never cleaned means, there is a leak somewhere - some objects still keep hardreferences to classpath elements even after the project is closed. *** This issue has been marked as a duplicate of 46550 ***
Reorganization of java component