docs: fix CLI reference, programmatic API example, and without-openapi syntax errors

[Copilot]

Summary

Several documentation pages had stale, incorrect, or broken content: the CLI reference was missing flags, the FAQ showed a wrong API signature, and the without-OpenAPI guide had invalid JS syntax and a broken link.

Original Prompt

Review the docs. Update any inconsistencies or errors and add missing details.

Manual acceptance tests

• docs/reference.md CLI table lists all flags from npx counterfact@latest --help including -p, --prune, --no-admin-api, --admin-api-token, --no-update-check, and --config
• docs/faq.md programmatic API example uses the Config-object signature matching docs/features/programmatic-api.md
• docs/features/without-openapi.md "reference guide" link resolves and the JS examples use valid export function syntax
• docs/features/programmatic-api.md "Return value" heading and table render as separate elements

Tasks

• docs/reference.md: Added missing CLI flags (-p for --port; --no-admin-api, --admin-api-token, --prune, --no-update-check, --config); fixed descriptions for --generate and --watch to match actual help text; used — instead of false for boolean-negation flags
• docs/faq.md: Replaced incorrect counterfact("openapi.yaml", "api", { port, serve }) call with the correct counterfact(config: Config) form
• docs/features/without-openapi.md: Fixed export const GET() { → export function GET() (invalid syntax); fixed [usage guide](./usage.md) → [reference guide](../reference.md) (file didn't exist at that path); removed duplicate "so that so that"
• docs/features/programmatic-api.md: Added missing blank line between the ## Return value heading and the Markdown table