newproject: add template-backed research project scaffold

[nsmiller2501]

Summary

This PR expands /newproject into a template-backed research-project scaffold.

What changed

• Adds local templates for CLAUDE.md, config.do, config.py, config.R, and requirements.txt.
• Updates the generated scaffold to include language-specific config files, agent_memory/, correspondence/, output/logs/, and references/raw/.
• Updates the newproject documentation to match the expanded scaffold.

Why

The goal is to keep generated projects organized from the first session while keeping root CLAUDE.md lighter: durable project memory lives in pointed-to files under agent_memory/, and reusable path setup lives in the language-specific config files.

Testing

• Reviewed the branch diff against the PR notes.
• Verified the PR branch contains only newproject files.
• No automated tests were run; this is a skill/documentation scaffold update.