refactor(spec): generate batch prompts in process

[n3sRan]

Summary

• expose batch prompt generation as an in-process function
• replace the Stage 6 subprocess invocation with a direct function call
• stop copying the prompt generator and file_utils.py into project workspaces
• preserve existing prompt, manifest, resume, and CLI behavior

Validation

• compared generated prompts and manifests against the previous subprocess flow
• verified fresh, resume, cycle, dry-run, and failure scenarios
• ran Python compilation and import checks