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Clarify Codex instruction sources
Co-Authored-By: Paperclip <noreply@paperclip.ing>
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@ -40,6 +40,12 @@ pnpm paperclipai agent local-cli codexcoder --company-id <company-id>
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This installs any missing skills, creates an agent API key, and prints shell exports to run as that agent.
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## Instructions Resolution
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If `instructionsFilePath` is configured, Paperclip reads that file and prepends it to the stdin prompt sent to `codex exec` on every run.
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This is separate from any workspace-level instruction discovery that Codex itself performs in the run `cwd`. Paperclip does not disable Codex-native repo instruction files, so a repo-local `AGENTS.md` may still be loaded by Codex in addition to the Paperclip-managed agent instructions.
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## Environment Test
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The environment test checks:
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