TypeSchema: Remove NestedIdentifier from Identifier union

[ryukzak]

Summary

• Remove NestedIdentifier from Identifier union — Identifier now contains only 7 non-nested kinds
• TypeIdentifier = Identifier | NestedIdentifier (introduced in base branch) becomes the wider alias
• Export LogicalIdentifier
• extractDependencies now filters out all nested identifiers from dependency lists
• Split transformFhirSchema into separate profile/specialization branches for correct typing
• Add nestedIndex fallback in resolveByUrl so constrainedChoice resolves nested types
• Remove dead isNestedIdentifier/kind === "nested" branches in TS writer
• Add as SpecializationTypeSchema casts in Python, C#, and tree-shake for NestedTypeSchema ↔ TypeSchema boundaries

Before (dependencies included nested identifiers):

dependencies: [
    { kind: "resource", name: "a", url: "uri::A" },
    { kind: "nested", name: "foo", url: "uri::A#foo" },
]

After (nested identifiers filtered out):

dependencies: [{ kind: "resource", name: "a", url: "uri::A" }]