I have attempted working with BinDiff to compare files and save the output, but unfortunately I am unable to save it to anything other than a .BinDiff or .BinExport file type. To try and counter this problem I attempted using another IDA plug-in, PatchDiff2. I am running into the same problem with this software. I can get the comparison and it is exactly what I want but I have no means of sending it to a text,pdf,or html file (which  I need it to be). I am running IDA 6.5 PatchDiff 2.0.10b and BinDiff 4.0. EDIT: I understand that this is open source, however I am wondering if there is a built in plug-in to simply save the results as a text file, pdf, html etc. 
PatchDiff2 Outputting results to a Text File
ida;idapro plugins;patch reversing;tool bindiff