I just use TexStudio. I don't use proper tex files, but it never complains unless I were to try and compile. But their navigation tree and tabbed interface for multiple files makes organizing things really nice.

I can have multiple instances at once, and it's all managed via files and my filesystem.

Eventually I want to build a web frontend to index and reference my data, but for now the above approach is working well.

Unlike Obsidian, TexStudio is open-source, which I consider a plus.