C4.5-auto-parm is a wrapper algorithm that runs a search over the possible parameter settings for C4.5 and tries to pick the best one for the given dataset. You can decide which parameters to vary by setting the AP_VARY_X options, where X is either M,C,G, or S (see quinlan-c45 for the meaning of these options). Almost all options applicable to the FSS search (Section 5.3) are applicable here with the AP_ prefix instead of FSS_ prefix. The search space explored is dumped into the file AP.dot and can be viewed using dot or dotty.
The algorithm was reported in kohavi-john-c45ap, although some changes since then mean results won't exactly match. Specifically, we do not add and subtract 5 from the array of possibilities because the reviewers considered this a bad hack. Also note that AP_CV_TIMES was set to 0 in our experiment, which takes more time.