References that are not literature or qualified sources The Duale Hochschule has published this guideline (German) (this question might be specific to the studies in Germany) and it does quite a good job explaining how literature shall be cited and put into a bibliography.

Now, in the evaluation sheet for the paper and thesis, literature research is mainly judged by its academic character, i.e. it should be primary sources, qualified links etc. I'm fine with that as well. My students should try to find and understand primary literature.

However, here's a caveat: the studies is Informatics. When they implement an application, the students use software libraries. Personally, I'd like to know the sources of those libraries, because some of them are not unique by their name.

I can understand that the students don't want to put them into bibliography, because they might not be scientific or academic, they are just a tool. However, there are sentences like


  To get around problem X, I use library Y.


IMHO, such decisions are ok, they don't require special research. Other researchers may simply use a tool ("hammer") to solve a problem without thinking much about it as well. Not mentioning such a library fix would leave others in a situation where the paper is not helpful.

How to deal with that situation and why? 

Should the software libraries 


be part of the bibliography, 
get their separate list of "software" references, 
just be mentioned in a footnote when the library name first occurs,
not be mentioned at all
...
As a computer scientist, I often encounter this as well. I have seen three main approaches used, in decreasing order of preference


Cite the paper about the software, if one exists: academic software is often the subject of papers, and the authors very much appreciate those citations, often explicitly requesting them in the software documentation.
Cite the software as a miscellaneous reference: most citation styles will have an explicit recommended means for doing so, (e.g., this post on APA software citations)
The first time the software is mentioned, put a link to the software in a footnote or parentheses.


The earlier ones are better for the authors of the software, but I have sometimes had journals refuse to allow me to give a proper citation.