Also fyi, bibtex support is one of the ideas for this years google summer of code application. This isn't a guarantee, but it's definitely on the radar.
My 3 cents..... about 'why joplin works for me and where' vs atom vs others.
Background:
android phone and tablet, on average 8h+ daily if I'm not on laptop
linux fedora desktop, now laptop
work lap were win and mac so far
Atom+git and joplin fulfill these needs:
good linux desktop app that I really like to use
outliner/hierarchical note taker without limits so far on depth
MD support - I love Joplin approach more - toggle for additional options which are all laid down at one place
ability to customise look & feel, especially MD formatting so that things can pop out better
Joplin additionally fulfills these needs:
editing available in mobile app
use for personal notes / that I want on all of my devices
bullet journal of lists and todos
posts or emails that are work in progress, in order not to lose them bc of wrong click, especially when I work on their translations
archive of conclusions about health things, also for cats
various household tips&tricks, appliance shopping research
log files for medications, memory/log for trip, concerts, other thoughts/diary
for work notes, without syncing anywhere
bullet journal of daily/weekly plan, and general wishlists
per issue details - research, or code snippets, solutions, links, questions to talk with others...
Atom + git fulfill these:
having separate files, I want my python script to be stand alone, and pics browsable in image viewer
plugin to paste screenshot and show it inline
more archival use
lecture notes (coursera, edx), other learning notes and meetups
tech tips&tricks and how-tos
job applications
with git I have access on mobile, to look up things, but I don't need to edit those on the go (official github app still doesn't allow edits anyway)
I want to sit down at a computer and be fully engaged when taking those
To me, they're almost the same in what they offer, and unlike many on this topic, I don't find one that much lacking in editor capabilites from the other.
However I don't use at all:
web clipping - c/p of parts is enough, and I prefer my formatting
tags - I like my folder structure, my brain can remember it easily
search - notes are my thoughts and ideas, so, written mostly from scratch, and serve as an extension to my brain, so I usually just know where something is, plus I have them highly organised
preview - I like coloring of MD in editor and that's what I need and like, no WYSIWYG
manual formatting - too slow, also I don't like keyboard shortcuts, just more things to remember, MD is the best for me
any as an IDE - my IDEs of choice are from JetBrains
I don't see myself going back to any of those solutions I've used in the past years, since they don't fulfill my needs and wants anymore.
This current joplin/atom+git combo does for a few years so far, and with both having plugins, I can't imagine what I'd want that wouldn't be possible to do in any of them.
I haven't used tags a lot in the past. I am using for status now though.
stub -- for things that are placeholders and haven't even begun to be drafted yet.
draft -- something that is being drafted
done -- something that is in a certain state of completedness. I am considering dropping this tag because it represents the desired state and if the document has no tag, I could just assume it is an item that I consider done.
Some others I have considered:
review -- something that I need to come back to
urgent
toss -- kinda like review. Something I am considering tossing, but haven't yet.
I think that is it. I am still playing with tags. I have hundreds upon hundreds of notes and documents within Joplin (I have been using it for years now). The hierarchy of notebooks tells me most of what I need to know about a thing. But it's state? That is an item of information that spans the whole thing. I don't want state notebooks. It would get ugly fast and be repeated everywhere. I have done that with the title but . . .
Anyway. That's what I have been doing of late. Hope it is useful.