This is what I learned from designing data architectures: If your data is variegated in format and form, don't look for a single tool/method solution to organize them. There is no single all-purpose organization method. Don't start with figuring out a method to organize your information. You will end up overengineering your org method. Instead, organize your information per "use-case". Start with a specific use-case/…
I endorse the idea that over-engineering is counterproductive. Focusing on principles over tools is good; tools come and go. My list of lessons learned (which has some overlap with yours) is: 1. Make sure your files and their organizational scheme can be transferred between tools. Your files need to be searchable, and at some point you will need portability. Text-based notes are easiest, but formats that have ubiquit…
- things I want to (re)read next
- "best" / "mind-blowing" technologies, usually built around a simple, minimalistic, but powerful concept (e.g. reagents for composable lock-free data structures, parallel prefix sum, Futamura projections, etc)
For everything else full-text search in Zotero has served me well.
About portability between tools I would go with Pandoc, it supports conversion between a number of Wiki formats and markdown, which should suffice for most purposes. Definitely avoid tools that lock you in their proprietary formats.