Zettlr, available at Zettlr.com, calls itself "one stop publication workbench". I find it just a good app to get yourself organized
To put it simply, Zettlr is a Markdown editor that allows for easy cross-linking and hierarchical file organization. On the left, you have a "workspace" file manager that shows you all the files with folders. In the middle is the main editor window with tabs so you can handle multiple files. On the right is extra info, such as outline view, linked view, external references, and so on.
Markdown is just plain text with some simple tags added, so that's very easy to learn and the app is quite fast even on slow hardware.
Zettlr has some extra powers such as Zotero integration for citations. Need to cite an internet article? Use the Chrome plug-in to add it to Zotero, edit it to add some meta info in Zotero, then you can cite it in Zettlr full Academic style. In fact, that's why Zettlr calls itself one-stop publication workbench... you can write your notes and your articles in Zettlr, then export it to LaTeX and have it published.
But Zettlr is also an excellent way to implement Zettelkasten (German for "slip box"), aka "digital second brain", where various bits of knowledge, with cross linking, and citations, becomes a creative cloud of inspiration for you to write papers and articles... once you've built up the contents. The more entries in the slipbox, and the more cross-linked they are, the more they should inspire you to write.
If you want to implement Zettelkasten in Zettlr, start by creating a folder, call it Zettelkasten if you want. Under that, create 3 folders: Fleeting Notes, Literature Notes, Permanent Notes. Please research Zettelkasten on how you actually use those folders.
Zettlr has many other power features such as templates/snippets and projects that's beyond the scope of this article.
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