For the record, this is what I did to test the Autophonemicizer on 21Dec12:
My test file was l-affric.xml.
I checked the first few already-edited entries, and no problems had been introduced by the autophonemcizer.
Then I carefully checked the transformation on lines 1811 to 2596, and cut-and pasted the correctly transformed pron:segs and hyphs into the main file. (I already did the quotes in this file on 13Dec12.) There were a couple of problems due to typos in the inputs, but nothing that we could have predicted or improved.
Then I pasted the rest of the autophonemicized file into the main l-affric file, so it is done.
Martin ran the autophonemicizer on all files with status="unedited" and status="rescued" on 24Dec12. Besides l-affric, the ones with status="editing" and status="additions_needed" are lexical suffix and affix files. In these, the prons are all already edited, the hyphs have been commented out, and the quotes will eventually be commented out too, so there is nothing to be gained from autophonemicizing these files.