Documentation refresh: update CLAUDE.md, SPEC.md, docs/ after cleanup

[osilkin98]

Context

After the repo cleanup removes ~15,000+ lines of code, documentation will be stale. This issue tracks the final documentation sweep.

What to do

Fix known doc bug

• docs/configuration.md states credential profiles use os.environ.setdefault() ("env vars win"), but factory/user_config.py:164-166 does os.environ[k] = v (unconditional override)
• This contradicts both reality and CLAUDE.md, which correctly documents the override behavior
• One-line fix, zero risk

Update CLAUDE.md

• Remove references to removed modes (improve, research, meta, founder, refine, etc.)
• Remove runner-switching documentation (bob/codex/opencode sections)
• Remove references to removed subsystems (dashboard, ACE, telemetry, notify)
• Update Architecture section to reflect simplified 4-layer system
• Update "Running the factory" examples to only show create/design/refactory/outer-loop
• Update environment variable documentation

Regenerate SPEC.md

• Run factory spec generate to rebuild from the pruned codebase
• Verify it accurately reflects the simplified architecture

Update docs/

• Remove or update docs/configuration.md sections about deleted config fields
• Update docs/index.md — remove runner comparison content
• Delete docs/codex-mcp.md if not already deleted in Delete dead runners (bob/codex/opencode) and runner infrastructure cleanup #1345
• Delete or rewrite docs/runner-v2-spec.md
• Update factory.md smoke test if it references dead runners

Update README.md

• Update CLI Quick Reference section to match surviving commands
• Remove references to removed modes and subsystems

Related

• Depends on all deletion issues completing first
• Research found 29 of 40 FACTORY_* env vars are undocumented — this is a separate issue (env var index) but could be partially addressed here