refactor: Enforce facade pattern for query/ module

[zharinov]

Summary

• Rename query.rs → stages.rs to fix module inception lint
• Make all submodules private, expose public API via pub use re-exports
• Update all internal imports to use the facade (crate::query::X) instead of reaching into submodules

Why

Enforces encapsulation: internal file structure is hidden, refactoring freedom is preserved, and the public API is explicit in mod.rs.