See also intent-specific workflow tips at, e.g. latex, academic writing.
What scope is my current document?
I don't know, run
Editor: Log Cursor Scope.
symbol-tree-view for bearable navigation between definitions.
teletype enables generic live collaborative document editing
tl;dr if a pane has an italic header, double click on it to keep it.
Not an extension, but be aware the pending pane feature is handy but will confuse the crap out of you if you expect Atom not to try to guess whether you want to look at a file temporarily or permanently.
Atom as a platform
People can and do build whole IDEs in atom.
hydrogen turns atom into an interface to jupyter kernels, for live code inspection and execution.
Juno is an IDE for julia which I don't particularly like.
Nuclide is Facebook's extensions to atom for web-centric development. I don't use it because I've served my webdev time, but web people might care about it.