The first paper is not complaining about FreeBSD, it's complaining about open source software in general, using the FreeBSD ports tree as an example. All of the software examples given are equally valid for Linux -- libtool and all its ugliness is still required, a lot of intermediary libraries are thrown out in the end result -- and the lessons are still unlearned. The mess of OSS begat ALSA, obstinate kernel developers refusing to do the right thing with ALSA begat PulseAudio, etc. Yes, commercial software sucks, but that does not excuse just how much of an unholy mess open source software is.