I think the title was too glib now, but it at least sparked some interesting discussion and exposure to Indigrid.

I tried doing everything in one mind map (task, reference management, lists, tracking, notes etc) and that got overwhelming.

I've now moved on to having a unifying org system/naming scheme over an array of specialized software. Much smoother.

washere wrote:

I installed, used for a while and uninstalled TheBrain many a times.
IMHO the mega mind mapper was just the usual hype and worse a time
killer for me, maybe OK for footnotes/research refs but there are much
better specialist in that genre. I used TiddlyWiki a lot until early
last year, then like the other wiki maker ConnectedText, I stopped using
it. I found a couple of other better wiki makers but have no use any
more for general purpose wiki files. More specialized these days, more
focused in each tool area.

The OP title is specific, not just one genre, mind-map or just wiki etc,
but one that ticks the boxes listed. The tool sought by the thread lists
the first 2 requirements as a "text file" app and then an "outline"r etc
etc. Interesting to see if there are any candidates proposed that not
only will tick all those boxes but are good enough to be "The One". I'm
not searching anymore, will be surprised if there is anything new
proposed I never heard of. Scrivener plus Scapple comes close, but they
are not the one either. I assume to remain on-topic, candidate tools
need to tick those genres he listed, presumably. It is in daily and long
term usage that one discovers the dark horse, the dirtied golden fleece,
the unassuming one.