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installCodexConfig() applied a narrow path-only regex pass before generateCodexAgentToml(), skipping the convertClaudeToCodexMarkdown() + neutralizeAgentReferences(..., 'AGENTS.md') pipeline used on the .md emit path. Result: emitted Codex agent TOMLs carried stale Claude-specific references (CLAUDE.md, .claude/skills/, .claude/commands/, .claude/agents/, .claudeignore, bare "Claude" agent-name mentions). Route the TOML path through convertClaudeToCodexMarkdown and extend that pipeline to cover bare .claude/<subdir>/ references and .claudeignore (both previously unhandled on the .md path too). The $HOME/.claude/ get-shit-done prefix substitution still runs first so the absolute Codex install path is preserved before the generic .claude → .codex rewrite. Regression test: tests/issue-2639-codex-toml-neutralization.test.cjs — drives installCodexConfig against a fixture containing every flagged marker and asserts the emitted TOML contains zero CLAUDE.md / .claude/ / .claudeignore occurrences and that Claude Code / Claude Opus product names survive. Fixes #2639