I assume that the libre software being referred to here is the GNU licensed software (which includes GNU/Linux).
The problem with the GNU license, as many have noted, is that it has this viral characteristic. If you include any GNU software in your application then the entire application becomes software that must be licensed under the GNU license.
This is also a huge body of software that is licensed under the Apache, MIT and Berkeley UNIX licenses. These licenses allow you to use the software, while still not making your software GNU licensed.
nderground is built on open source software, but none of it is libre software (GNU licensed software). We want to recover our investment in the years of work that it took to create nderground. We have stayed away from anything that carries the viral GNU license.