I end up taking notes in a text file daily, with un-resolved or in-progress items at the bottom. They get pushed downward linearly until they are finished, at which point they get immortalized in the greppable daily log that gets deposited above my "working area" somewhere toward the tail of the file. Requires a lot of discipline and doesn't have a lot of structure, but having the "working area" next to the journal has served me well. I use vimwiki[1] for most of the editing, in addition to custom scripts written using pandoc[2] for things like billing/reporting.
The biggest help has been having custom constructs such as "```timekeeping" blocks to contain time logs, and also having a "clean-out" ritual where I archive things once in a while.
[1]: https://vimwiki.github.io/
[2]: https://pandoc.org/
