I am a historian, teacher, and a writer. I am looking for the best note-taking app for my use-case — Or in this case a second brain.
markdown (preference for multi-markdown)
note linking capabilities (active within app preferably)
My issue is this. Whether I am writing, researching or teaching I want quick access to evidence/data. I want to be able to catalogue data in a way that allows quick retrieval but also to be able to link notes together directly so that I can click the link directly in the note. In essence I am looking to create a plain text database with powerful search functions and note linking. One huge use-case for me is that I don’t lecture in my classroom and I need a quick method of accessing data on the fly so that I can answer student questions in real-time. This works relatively well in the app I already use, Bear. But I am not particularly fond of the “folder” (tag) management. I love tags, but not sure as a primary mode of organization. I am flirting with Ulysses (since I have a setapp subscription).
How about DevonThink ? It has excellent organizational (folders, tags, and search) capabilities. You can write in markdown and create document links (within and out side the program). I use the Archive for things that I am pondering and leave my primary references and notes in DevonThink - but it is quite easy to link the two.
I second the recommendation by @NiranS of DEVONthink Pro. It is a very flexible database app for macOS and iOS that can sync data (though I only use the macOS app). DEVONthink can either “import” files (that is, manage files in an internal folder structure in its own database package) or “index” files (that is, work with files that are stored outside the database package but indexed by the database).
I choose to “index” files in DEVONthink Pro so that I still have full control over the indexed files in the macOS filesystem, and I can also browse the files in other apps such as the Finder, Terminal, or Leap, creating what Douglas Barone in 2009 called the “file system infobase manager”: “rather than putting data into an [‘everything bucket’] application and using the ho-hum functions of that app to work with my ideas, I keep my data separate and have best-in-class applications, using higher levels of functionality, work on it. […] By using ‘everything bucket’ applications you give up functionality for compactness and eventually that equation works against your creative process. By working in the file system you use the best app for each specific purpose.”