docs: comprehensive README update and fix /setup alias conflict

[laynepenney]

Summary

• Add missing CLI options to documentation (8 new options)
• Document /init command for initializing Codi config files
• Add missing command sections: Usage & Cost Tracking, Planning, RAG, Approvals
• Expand .codi.json example with all major config options and add configuration table
• Add missing tools to documentation: insert_line, list_directory, print_tree
• Remove conflicting setup alias from /init command (was shadowing /setup)
• Fix RAG embeddings test to match current Ollama-preferred auto-detection behavior

Test plan

• Build passes
• All tests pass (1419 tests)
• Verify README renders correctly on GitHub

🤖 Generated with Claude Code

[laynepenney]

Self-Review Complete

Reviewed the diff - all changes look correct:

• README.md: CLI options, commands, tools, and config sections all updated accurately
• config-commands.ts: Removed setup alias from /init to avoid shadowing the /setup command
• rag-embeddings.test.ts: Test updates correctly reflect the Ollama-preferred auto-detection behavior

Build passes, all 1419 tests pass. Ready to merge.