Ask HN: What do you use to organize your knowledge?

In a specific directory, I arrange notes according to subject in directories, and the script parses them and spits out HTML files that displays them in a fashion I find useful. With MathJax, I can render LaTeX. It also spits out an index files so I can see at a glance my subjects and notes on those subjects.

I've been giving some thought to doing something more involved, so I can get full text search capabilities from the index page. It's something I play around with every so often as the inspiration hits me. I will not be surprised if this posts leads me back to playing with it for a bit, although I am busy for the upcoming week already.

You can trivially get something similar with something like vimwiki [0]. The only reason I went further was that I wanted greater levels of customization.

[0] https://code.google.com/p/vimwiki/

Edit: The full text search from the index is just a nicety given the way I like having the notes displayed. I can already grep from the command line, of course. I have other ideas about nice-to-have dynamic behaviour, but a lot of the stuff falls into the lower percentages of the 20% of the 80-20 split.

In The Pragmatic Programmer, one of the tips advocates keeping knowledge in plain text:

> Keep Knowledge in Plain Text

> Plain text won’t become obsolete. It helps leverage your work and simplifies debugging and testing.

The full text expands on the benefits, such as searchability and other stuff I can't recall at the moment.

I try to stay as close to possible to plain text as I can. Even Markdown is a bit heavy for the task, although I have given some thought to adopting it and avoiding needing any custom parsing.

Lastly, I wasn't clear why I output to HTML. I put them up on a server so that I can access them remotely. I can also upload notes, or input a quick note to a textarea and submit it. It's device-agnostic; I just need a browser. I haven't bothered to implement making currently existing notes editable.

As soon as Simplenote allow font changes, I'm going back though for the Android cross platform support.

Realizing that there is no such system/app I split things out:

* Important Stuff as well as trivia -> CalDav... believe it or not, but CalDav beats most other systems/apps out there, it's accessible on almost any device and you usually have a wide variety of applications to edit your "calendar events", use different calendars for important vs trivia

* Stuff you read on the internet -> obviously (synced) bookmarks (firefox, chrome, opera and others have builtin sync)

* Ideas, plans, drawings -> A5 pen and paper notebook (most people will advocate moleskine, I prefer Leuchtturm notebooks (to each his/her own)

* Research, papers, references -> good old text files, index + txt + pdf + bib (vim + vimwiki + git + some zsh alias like wiki="cd ~/wiki/; git pull; vi index.wiki; git commit -a; git push; cd -")

So far, this works quite well, although I have to admit that while separation is king, it also hinders creativity at times, so I'm slowly starting to integrate other things into the wiki (write firefox bookmark and caldav importer/parser, thinking about scanning/digitizing notebooks...) to be able to cross-reference things. The long term goal is to create a visualization that allows me to visualize (duuuh) all this data in different ways (especially useful for research and connecting the dots).

Hope this helps and I would really be interested how others manage this, especially regarding research, papers etc (Mendeley and others just aren't flexible enough for me...).