refactor: five architectural deepening improvements

Candidate 1 (NormalizedGraph): qualify→resolve→filter is now a single
named operation returning a distinct type; raw CodeGraph cannot call
module_edges/subgraph_by_module — pipeline order enforced at compile time.

Candidate 2 (Use cases): GenerateDiagram, CheckFreshness, DiffDiagram
extracted to application/src/use_cases/; presentation is now a thin CLI
dispatcher (~100 lines less, three fewer local functions).

Candidate 3 (ExtractionContext): shared accumulator for both Rust and
Python extractors replaces parallel Vec<> + 4-arg passing chains.

Candidate 4 (ModuleAssignment): ModuleName::assign() returns
ModuleAssignment { Explicit | Inferred | Unresolved } instead of Option,
callers can distinguish resolution strategies.

Candidate 5 (SplitRenderer): append_cross_module_deps removed from
DiagramRenderer port; replaced by render_for_module() default impl —
port interface now reflects what all renderers actually share.

crates/application/src/lib.rs

@@ -1 +1,2 @@
 pub mod queries;
+pub mod use_cases;