I've addressed many of those problems with a bunch of different tricks:
- I have a simonw/notes repo which will NEVER be public, which is for me to put issue threads in for things that aren't part of one of my other repos, or that I want to keep private. I sometimes change my mind and transfer issues out into other repos using this trick: https://til.simonwillison.net/github/transfer-issue-private-...
- I frequently run searches across every issue in my "simonw" GitHub profile, which covers both my public and private issue repos
- For tying issues together, I use GitHub Projects - which can contain issues from multiple repos in a single place. I use that for my personal TODO list, and for collaborations with other people that span multiple repos.
- I link issues together a LOT - if you add a "- #123" Markdown bullet point list in a GitHub issue comment it will turn each bullet point into a fully displayed link to the referenced issue, including its open or closed state.
- You can use this for checklists too: "- [ ] #123" will turn into a checkbox which automatically checks itself when the referenced issue is closed.
- I use GitHub labels for things like "Research" to mark issues which are longer running research things as opposed to active bugs or features.
GitHub is nice but starting about a year ago I have been asking myself "what if they lock me out of my account" for online services and there is no good answer.
Obsidian plus a data query plugin can do most of the stuff you've described but my data isn't at the mercy of a 3rd party, so that's what I go with.
Yeah, I worry about that too. I have SO much of my stuff dependent on my GitHub account now.
I'm slightly reassured by how useful their APIs are. I have automated exports of a lot of my GitHub issues, though I really should shore those up and make sure I'm capturing everything.
- I have a simonw/notes repo which will NEVER be public, which is for me to put issue threads in for things that aren't part of one of my other repos, or that I want to keep private. I sometimes change my mind and transfer issues out into other repos using this trick: https://til.simonwillison.net/github/transfer-issue-private-...
- I frequently run searches across every issue in my "simonw" GitHub profile, which covers both my public and private issue repos
- I also built https://github-to-sqlite.dogsheep.net/github/issue_comments - a separate Datasette search interface across 10,000 issue comments from my various repos. I use that a lot less now that GitHub search has improved though.
- For tying issues together, I use GitHub Projects - which can contain issues from multiple repos in a single place. I use that for my personal TODO list, and for collaborations with other people that span multiple repos.
- I link issues together a LOT - if you add a "- #123" Markdown bullet point list in a GitHub issue comment it will turn each bullet point into a fully displayed link to the referenced issue, including its open or closed state.
- You can use this for checklists too: "- [ ] #123" will turn into a checkbox which automatically checks itself when the referenced issue is closed.
- I use GitHub labels for things like "Research" to mark issues which are longer running research things as opposed to active bugs or features.