Thanks for your excellent job.
But I found a bug in Amalgam. In file https://github.com/exatoa/Bench4BL/blob/master/techniques/AmaLgam/src/org/amalgam/analysis/CodeRepository.java line 255, "if (!fileHistories.containsKey(fullClassName)) {", fullClassName should be fid. I guess for the BugCache, you used the wrong file history, where only one commit for each fid.