We have Bamboo which I would consider the worst of the Atlassian stack. Access rights, submodules and remote agents don't mix well.

I like Confluence, I hate some pre/styled things they do, but in general is not a bad wiki software and it's integrated with Jira. The worst is no one at my company reads these docs :)

I administer my company's internal Confluence server and author most of the content, and I have a few complaints but overall I love using it. What do you dislike about it?

My 2¢: Confluence's primary job is to share and manage lots of written documentation. If I wanted to make such software I'd make it fast, the curation/management job lightweight and inline, and emphasize readability and promote fast comprehension of information with layout and design.

Confluence is slow, curation/management is ponderous and the design ignores hundreds of years of research / practice in visual processing of information.

My biggest complaint is that it doesnt support markdown correctly.

For Confluence: we've found a much better alternative is Quip - we all love it after the switch. Dropbox Paper is another new alternative that people seem to like.

JIRA is horrendous. The search is a pain.

Probably the only end user software you need to look at the documentation to do any search but a simple keyword search

I would rate them the other way around, barely...

Which is sad because the pre-acquisition confluence wasn't even bad...

It still isn't. People just like to complain about popular things on HN.

I do think it's bad now. It crossed the line with the removal of markup editing.