+ feat: apply CLI options from JSON

[baocang]

Summary

• make the existing --options <json> flag apply CLI options for module and generic CRUD commands
• let explicit CLI flags override values from the JSON object
• preserve JSON filter/search values when Commander contributes empty-array defaults
• reject malformed JSON and non-object values with E2009 before authentication
• document the option and its precedence

Verification

• bun run typecheck
• bun test (197 tests)
• bun run build
• git diff --check