The title contains the reason on why we created Fiji (http://pacific.mpi-cbg.de): so that instead of releasing a Matlab script without documentation on its many parameters and exact Matlab version used, as a print out (or nowadays, downloadable .m file as supplementary material), we could offer instead a ready-downloadable, version-controlled and fully working program.

A colleague of mine made similar remarks recently:

"... if you can’t see the code of a piece of ... software, then you cannot say what the software really does, and this is not scientific."