In last night's nightly build, the parsing regressions are still present (no change at all).
I will send pointers to the profiles separately. To summarize, in parseDomainXML, the time breaks down 65% to org.jvnet.hjk2.config.ConfigParser.handleElement (though a long series of recursive calls) and 29% to DomDocument.getModelByElementName (though a series of recursive calls to DomDocument.buildModel). In previous builds, the recursion chain for handleElement is much shorter and the entire sequences takes 1/100th the time as current builds (well, the profiling overhead will have affected that to some degree...); previous builds also show no recursioon to buildModel. So either the recursion chains here are for some reason much longer, or the methods themselves are taking longer and the sampling catches the recursion now that it didn't used to catch.
In the Transaction.commit(), the bulk of the time (44%) is in DescriptorImpl.getRanking, which is used by TreeMap.put; that entire chain of creating the IndexedListData.getSortedList is 62% of the time. 11% of the time is spent in ServiceLocatorImpl.validate, 5% in ServiceLocatorUtilities.addOneDescriptor, and 5% in Transaction.canCommit.