Texpad 1.3.1 made it to the Mac App Store a few days ago. In it we added support for typesetting Makeindex/BibTeX simultaneously, we added support for Biber and we fixed a couple of bugs introduced in the 1.3 rewrite including the shell escape flag.
Meanwhile we have finished Texpad 1.4, the highlights of which are editor themes, custom build scripts(more on these to come) and global search. Also, we fixed a remaining BibTeX problem, sped up the parsing and plugged a memory leak. 1.4 has just been submitted to the App Store and it should be available 7-10 days from now.