Obsidian (
https://obsidian.md) is the only tool I e found that didn’t try and force me into a specific paradigm and let me develop an organisation for my disparate collections of notes and material much like you describe.
It’s own paid upgrade feature/service offers a cross platform sync that handles a couple of gigs of basically any type of document and is encrypted client side. At a price I’ve found perfectly acceptable for the excellent quality of service and as a way to support the ongoing development of what is otherwise a free program. It also works offline and does opportunistic sync so well I bought a PineNote e-Ink tablet primarily because I knew my note workflow wouldn’t be crippled by the device not having cellular data for immediately synchronising changes. Mac, android, iOS, desktop Linux, x86, arm, windows everywhere I’ve needed it I can get my documents.
I definitely recommend at least giving it a try and exploring the plug-in ecosystem to see if you can find a good set of workflows for your various documents and research. A few of the plugins are quite powerful and offer various visual management functionality like tag and link graphs, navigation features and other functionality. I don’t see myself being pulled away from it at this point and all I’m looking for is ways to better integrate other platforms with Obsidian because it definitely works for me.
