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There is a 2000 character limit in the question box, so here is what I'm using now: - pinboard for managing bookmarks (database of things that may be useful sometime; probably never) & reading list for articles - I'm testing tagspaces (http://www.tagspaces.org/) for local files organization (mostly tagging research papers and books; didn't like Mendeley) - cardav & caldav from owncloud for contacts and events - anki as a memorization tool (spaced repetition) - from languages to my own mistakes (i.e. "lessons learned", so I won't repeat them) - for insights, notes, ideas, things I've learned & everything else I use personal wiki (media wiki) on localhost. This is the biggest part of my "system", I have there entries like things to buy someday, current project's notes/resources, useful scripts, configuration snippets, notes from books, journeys, analysis of my own behaviour, personal journal, ideas for startups etc. But it's hard to organize, it becomes a mess very easly after some time. Also, I can't use it on mobile (I don't want to put all this on the web, there is a lot of personal info), it takes time to add new thing/entry (I need to think to which page new piece of information belongs etc.). - simplified version of gtd as a meta-system managing this system and for projects/things to do |
So I switched back to plain text, using the Markdown syntax format. Sync works fine with IMAP based email account (note apps on iOS & Android support that too). For visual complex documents I use a WYSIWYG HTML editor and the HTML format. SVN/Git repo to preserve the edit history. And I coded an desktop/enterprise search engine myself to search through PDFs, HTML and various Office formats - similar to the discontinued Google Desktop search and some enterprise search software.