fix(rust): honor explicit roots when indexing nested workspaces

[Cuiyus]

Explicit Rust indexing of a child directory currently selects an ancestor index. A different child model can be rejected against the parent, while scan updates or --rebuild can overwrite the parent's index.

Resolve index writes and remote-consent preflight at the requested root. Queries, status, and automatic refresh continue to resolve the existing index.

Add regression coverage for matching and different models, rebuilds, a loaded parent query runtime, workspace-bound consent, and direct/server CLI modes.

Refs #211 and #212.

Validation:

• Local cargo fmt --all --check, workspace/all-targets cargo check, Clippy with -D warnings, and engine docs with RUSTDOCFLAGS="-D warnings" passed.
• Rust npm packaging tests: 7 passed.