This is how to regenerate the 4Pane build setup. It's highly unlikely that you'll need to do so (thus the name of this file, which you ignored).

But if that unlikelihood occurs, the first thing to do is to transfer all this dir's files, except mydatafiles.bkl, into the main 4Pane directory i.e. ../.

Next, look in the wxWidgets source code for the build/bakefiles/wxpresets dir, and note its full path: you'll need it below. While you're there, copy wxwin.m4 (in the wxWidgets main dir) to the 4Pane dir.

Then you need to download and install bakefile (http://www.bakefile.org/). If you don't configure with --prefix=/usr, you'll probably need to symlink the two bakefile* files that get installed into /usr/local/share/aclocal, to /usr/share/aclocal.

Now in a terminal open to the 4Pane dir, you can do the following:
  bakefile -f autoconf -I /path/to/wxWidgets/build/bakefiles/wxpresets 4Pane.bkl
  aclocal  -I .
  autoconf

You should then be able to proceed as normal with ./configure