[codex] Improve CLI generation experience

[ItayTheDar]

Summary

• Adds the new pynest new, pynest add, and pynest doctor command surface while keeping pynest generate ... compatibility.
• Adds guided human prompts, styled terminal summaries, deterministic --json output, --dry-run, and .pynest.yaml project metadata.
• Switches generated apps to uv/pyproject.toml by default, with explicit --package-manager requirements support.
• Adds granular PyNest extras such as pynest-api[http,sqlite-async] so selected app stacks resolve the needed HTTP/ORM/database dependencies through one dependency.
• Updates docs, CLI tests, and CLI CI coverage.

Validation

• uv run pytest tests/test_cli -q -> 23 passed
• uv run pytest tests -q -> 189 passed, 9 warnings
• Local extra resolution check: pynest-api[http,sqlite-async] @ file://<repo> resolves and imports sqlalchemy, aiosqlite, and python-dotenv
• git diff --check -> clean

Notes

Unrelated websocket/gateway working-tree changes were left unstaged and are not part of this PR.