[smarks159]

I write a lot and have a lot of text files scattered all over my desktop with ideas, plans and notes. Everytime I start a programming project I also end up with a lot of text files with requirements, design decisions and implementation details. I kept all these ideas in plain text files because, none of the existing tools really fit what I wanted. I ended up creating a program to help with this based on the ideas of Doug Engelbart.[1] The program is still experimental and just deals with text at the moment but I still find it useful.

In terms of research papers, you may want to look at the ideas of Doug Engelbart. The process which you speak of, of collecting information and learning from it, Engelbart termed the CODIAK process. There is a section describing what CODIAK is in this paper[2]. (click on the CODIAK Process link in the table of contents). Engelbart speaks of this process in terms of groups and organizations, but the ideas apply to individuals as well. Engelbart's goal was to create an integrated "knowledge workshop", where all the different programs for organization everything would be integrated together and act as an extension of the human mind to augment people's abilities to collect and digest an ever increasing amount of information and knowledge. There is a lot of work left to be done in this area, but it is an important problem to solve.

[1] https://github.com/smarks159/hyperdocument-system-wiki

[2] http://www.dougengelbart.org/pubs/augment-132811.html#6