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SECURITY_REDACTIONS.md

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Security And Redaction Notes

This file records the content review performed for the public release scaffold.

Summary

  • No API keys, access tokens, secrets, or credentials were found in the copied public files.
  • No absolute local filesystem paths were found in the copied scripts.
  • No references to specific colleagues or private collaboration notes were found in the copied public files.
  • The original private repository was not modified during this process.

Script Review

  • The copied scripts use repository-relative paths derived from Path(__file__) rather than hardcoded machine-specific paths.
  • Several scripts reference private-workflow directories such as raw/, outputs/, indexes/, dashboards/, paragraphs/, prompts/, and templates/. Those references are architectural, not secret, and are left unchanged.
  • The optional local workflow scripts include references to claude and codex CLIs. These are tooling references, not secrets.

Sample Content Review

  • The approved sample files do not contain credentials, email addresses, or explicit colleague references.
  • The approved sample does contain a small number of references to non-included or provisional literature notes. These are cited as part of the methodology sample and are not themselves copied into the public repository.
  • Notable provisional references retained in the approved sample:
    • Carter_bioRxiv_2026.md
    • Rey-Millet_bioRxiv_2026.md
    • Lee_BiophysJ_2025.md

Redactions Applied

  • None at this stage.

Residual Risks

  • Some example pages intentionally link to notes outside the public sample. Those links reflect the private KB architecture and may not resolve inside this repository.
  • Some example pages discuss provisional or low-confidence evidence from non-included notes. That is methodological context, but you may still want to trim or rewrite those references before publishing if you want a stricter public boundary.