I'm not sure if Jira and other task tracking tools can be used just as well to document work done by intrinsic motivators though. I mean, yes, they _can_ be, but I don't think they're as good as they could be. In fact, I'd say there's a big gap in the market for a solution that gives non-technical managers some reassurance that progress is being made while also not getting in the way of the ad hoc workflows the post describes.
It wasn't always like that for me (document, bah! comments, bah!) but as I grow older I've come to appreciate the possibility to offload information in my brain to a more persistent media. This way I only keep the index in my brain ("Hey, wait a minute, I recognize this..."). Maybe I'm just lazy but I hate doing the same thing twice. I also hate saying the same thing twice so before I explain something to someone I like to write it down and give them a copy. Then when they ask me about it I simply refer them to the document (in a friendly (RTFM) manner).
What we have today is an almost complete lack of mechanical/repetitive work to measure.
That's not a tool gap but a trust gap in the team, and no tool can remedy that, IMO.
The first problem was thinking that you could set meaningful hard deadlines for inadequately defined goals. The second problem was acting as though they were meaningful.
Typically complex tasks are solved better in an environment with emphasis on intrinsic motivators.
It's not wissful thinking. It's a keen observation.
Basically management offloads the responsibility of actually managing to a process of accounting. It's a less skillfull, less productive, but a much more predictable form of management.
The problem was not the Jira. It was the new PM who instituted the cultural change. Jira can be used just a well to document work done by intrinsic motivators.