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This manual documents various tools for configuring Matlab based software using GNU Autoconf and GNU Automake. The project started while porting a huge amount of MEX-files from Unix to Cygwin. At almost the same time, I had to port the same MEX-files from HP-UX to Solaris and Linux. A few months earlier a new Matlab release was installed at our site and I learned that MEX-files are not compatible between different Matlab versions. So it was time to write some clever M4 macros for the GNU Autotools to figure out the portability bits automatically.