> You can't have an extension system that (...)
Yes you can. Extension systems of today have multiple problems that prevent that. The basic assumption that has to go, though, is that a core application like VSCode can be written once, then be extended to infinity without the core evolving. That's an assumption you see everywhere in extension systems, and it restricts everything to "features or security, but not both".
Taking your examples:
> run a locally installed linter
VSCode and its extensions have certain files opened. The linter can do much less if it gets read-only access to those files, but not write access and no other files, not the open internet or something.
This has then to be coupled with those permissions being displayed before installing, allowing them to be reviewed by users as well as plugin repo curators. Basically listing those permissions as declarative metadata.
Because then a user or curator won't see "this plugin can read and write all your files" but "this plugin can read (but not write) the files being opened by VSCode". If the plugin wants to exfiltrate those files, the permissions would also list "this plugin can send HTTP requests to totally-legit-site.ru" instead of "this plugin gets arbitrary internet access".
Main lession: permissions are WAY too coarse. But if they are fine-grained, they will soon no longer match the evolution of extensions, so the core system has to evolve too.
> view the status of docker containers
"This plugin can view the status of all docker containers started by other VSCode extensions in the same VSCode window".
> users will scream and cry about extensions being limited
Are those the same users? We might need two different products here, "feature VSCode" and "secure VSCode".