I suspect you may be operating in "Restricted mode," aka it doesn't know if it can trust the directory. In that mode, the main tools like Rust analyzer are quit

I suspect you may be operating in "Restricted mode," aka it doesn't know if it can trust the directory. In that mode, the main tools like Rust analyzer are quite restricted. All of your complaints should be resolved once Rust Analyzer/basedpyrite are up and running. I do think they should have a more obvious warning that the current directory is untrusted, right now the little green warning in the corner is way too unobtrusive and will result in many people having the same issue as you.