Although I'm pretty sure you have had thoughts in that direction, I wanted to mentioned something:
Regarding the first bullet point (official package file structure) I would also suggest some sort of version handling for the plugins, so the user is easily able to identify which plugin version he uses and in direction of auto install from Keypirinha also able to determine whether a plugin needs an update or not.
One idea could be to use the github REST API. If every plugin is placed inside a github repository which is linked in the manifest file, you can use the REST API from github to compare the internal manifest version with the latest release on github
I have planned to allow package versioning through the manifest file indeed. Mainly for manual check-up at the beginning. The automation of the install and update of packages will come later unfortunately. It's a matter of priority in the todo list. That being said, I hadn't thought of taking a look at the GitHub API so far so I'll keep that in mind. It was worth mentioning it, thanks!