These are basic instructions for recreating the project files:

Changing the version number:
----------------------------
build/autoconf/configure.ac
Line 9:	
AC_INIT ....

Change SO version
-----------------
muparser.bkl / tag <so_version>

Updating the make- and projectfiles:
------------------------------------
Clearing old project and makefiles:
bakefile_gen -c

Remaking Projects and Makefiles:
bakefile_gen

In addition to that automake must be started to create the new configure script:
rm -rf autoconf/autom4te.cache autoconf/aclocal.m4
../autoconf/acregen.sh

!!! IMPORTANT !!! 
When building bakefile from the tar.gz archive make sure to 
use the option --prefix=/usr wit the config file since its 
path will default to /usr/local. This would cause strange errors!