[edwintorok]

Some of these have been mentioned at various points:

https://zettelkasten.de/posts/three-layers-structure-zettelk... https://github.com/renerocksai/sublimeless_zk https://tiddlywiki.com/ http://journal.mcmorgan.org/view/incremental-paragraphs/ward... http://fedwiki.org/hack.platform.earth/fedwiki-for-notetakin... https://github.com/burtonator/polar-bookshelf

Perhaps a single system is not the answer, but a combination, e.g. for taking notes I'd pick fedwiki/sublimeless_zk/Zim/org-mode.

For organizing PDFs with full-text search Zotero is quite good, and you can link to your PDFs from your notes, but I wouldn't store my notes about PDFs inside Zotero (because then it'd be separated from my notes about non-PDF articles).

For keeping track of articles Firefox bookmarks (with Firefox Sync on Android acting as a 'read me later' bag).