refactor: Project manifest-derived repository facts (#13593)
## Intent
Remove package-change and workspace-path behavior selected by
contributor provenance.
## Changes
- Project real package.json-backed scopes from authoritative repository
definitions independently of `ToolchainId`.
- Route change ownership and JavaScript workspace path dependency
splitting through that projection.
- Compose accepted native change observations without reactivating them
by producer identity.
- Validate and stably deduplicate native change facts while preserving
JavaScript lockfile priority.
- Reject duplicate physical definition owners and root-manifest symlink
aliases during repository construction.
- Document the manifest-derived projection and change-observation
contract.
## Testing
- `cargo test -p turborepo-repository` (391 passed)
- `cargo test -p turborepo-lib package_changes_watcher` (44 passed)
- `cargo clippy -p turborepo-repository -p turborepo-lib --all-targets
-- -D warnings`
- Pre-push `format` and `check:toml` hooks
Advances TURBO-5798.
