refactor: Use package knowledge in repository views (#13459)
### Description
Part 4 of the package/scope knowledge completion stack.
Use authoritative scope identity and paths in query, `turbo ls`, and
devtools package views. Relationship and script payloads remain
unchanged, while structural graph roots are no longer exposed as
packages.
### Testing Instructions
- `cargo test -p turborepo-query`
- `cargo test -p turborepo-devtools`
- `cargo test -p turbo --test command_ls_test --test command_query_test`
