Detect runtime from execution_context path or env vars at workflow start,
then set INSTRUCTION_FILE (AGENTS.md for Codex, CLAUDE.md for all others).
Pass --output $INSTRUCTION_FILE to generate-claude-md so the helper writes
to the correct file instead of always defaulting to CLAUDE.md.
Also add .codex to skipDirs in init.cjs so Codex runtime directories are
not mistaken for project content during brownfield codebase analysis.
Closes#1521
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>