feat: add OpenAPI Overlays support

[Copilot]

Summary

Adds support for OpenAPI Overlays v1.0.0 — a mechanism to apply targeted patches to an OpenAPI document without modifying the original file.

New CLI flag (repeatable, applied in order):

counterfact openapi.yaml ./out --overlay base.yaml --overlay env-override.yaml

Overlay file format (my-overlay.yaml):

overlay: 1.0.0
info:
  title: My Overlay
  version: 1.0.0
actions:
  - target: $.info
    update:
      description: Injected by overlay
  - target: $.paths['/internal']
    remove: true

Per-spec overlays in counterfact.yaml:

spec:
  - source: openapi.yaml
    group: ""
    overlays:
      - base-overlay.yaml
      - env-overlay.yaml

Overlays are applied in both the code-generation pipeline (Specification.fromFile) and the runtime server pipeline (OpenApiDocument.load). deepMerge is guarded against prototype pollution.

Original Prompt

Overlays

Add support for OpenAPI overlays

Manual acceptance tests

• counterfact openapi.yaml ./out --overlay overlay.yaml applies the overlay's update action (e.g. changes info.title) before generating route stubs
• An overlay remove action suppresses route stub generation for the removed path
• Overlays specified under overlays: in a counterfact.yaml spec entry are applied on startup
• Repeating --overlay multiple times applies each file in the order given
• A missing overlay file exits with a clear error message rather than a silent crash
• Routes unaffected by an overlay continue to serve responses unchanged

Tasks

• Added src/util/apply-overlay.ts: loadOverlay, applyOverlayActions (JSONPath via jsonpath-plus), applyOverlays; deepMerge with __proto__/constructor/prototype guard
• Extended Specification.fromFile()/load() and OpenApiDocument constructor to accept overlays?: readonly string[]
• Propagated overlays through Config, SpecConfig, ApiRunner, CodeGenerator, and loadOpenApiDocument
• Added repeatable --overlay <path> Commander option to run.ts; per-spec overlays in multi-spec config entries; single-spec CLI flag falls back to config.overlays
• Added 17 unit tests in test/util/apply-overlay.test.ts
• Updated docs/reference.md with full Overlays section and CLI flag entry
• Added minor changeset