Taking notes is a fundamental technique in academic writing and since the advent of the Unix operating system lots of software was created for this purpose, right? It is a rhetorical question because the history of note taking software is not well researched. Sure in terms of quantity many attempts were made for creating notes. The most famous one are the emacs program, the texinfo hypertext format and the bibtex format. The surprising situation is, that none of these attempts are popular and most users are not aware of these tools.
Let us compare the situation in Unix with other operating systems like Windows. The situation in Windows isn't very different. On the one hand there are some dedicated bibliographic databases available like Endnote and Citavi and on the other hand there are text editors and the famous ms-word program for making notes. All these programs are not very powerful. For example in fixed bibliographic database it is not allowed to enter full text comments, while in MS-word like text editor it is hard to search full text in the information.
If all the existing operating systems and note taking software have a low quality and are not used in reality, what was used instead for creating notes in the past? The surprising answer is that note taking is not a big thing, even in academia the value is overestimated. To investigate the working thesis in detail let us describe how to write a paper without any notes or references.
What the author needs is some sort of typing tool which are mostly a classical typewriter or a pen or a software like MS-Word or LaTeX. Then the sentences are formulated. If the text was written some (not more than 3 bibliographic references are added) The exact description which includes the title, DOI number and the journal is retrieved from a library catalog. Then the text gets formatted into the PDF format and is printed on a laser printer. The interesting situation is, that during the entire writing process there was no need to create notes or recall existing notes. But the academic author sits in front of an empty sheet of paper and formulates what he knows about a subject.
The chance is high, that such kind of writing process was common in the past and was applied by the majority of authors. The content of the written text depends mostly on the individual knowledge about a subject. If the author is informed very well he can write a better text and vice versa. Basically spoken all the hype around note taking, outliner software and bibliographic file formats doesn't fit to the reality. For writing a normal academic text there is no need to get familiar with the bibtex software or with a high end free form database like MyInfo.
Even the famous writer and sociologist Niklas Luhmann wasn't using a dedicated note taking system. His so called Zettelkasten was mostly a joke. He has explained to his student that note taking is very important but he wasn't using the technique for himself. Most of the 90000 index cards from his scientific legacy were created only for the public to mimicry reading skills.