How to Clean Up Messy Documentation in Your Repo

William Warne

Software Engineer | Fractional CTO | Founder

Introduction

Repos that grow with AI-assisted development often end up with documentation everywhere: ad-hoc markdown, outdated READMEs, and no shared structure. Cleaning that up doesn't have to mean a big-bang rewrite. This post walks through how to clean up messy docs using the Documentation Management Pack—step by step, with clear "done when" criteria.

Step 1: Assess Your Current State

Before changing anything, map what you have. Where are docs today? What's valuable? What's noise or wrong? Use the pack's checklists to assess:

  • General document checklist — Does each doc have the right sections and structure for its type?
  • Document metadata — Document Information (type, version, status, date) present and consistent?
  • Tools and assets — Cursor rules, skills, CLAUDE.md present and up to date? Has ctx compile been run?
  • Traceability — Requirement IDs, 02→03→05→08 links, "done when" criteria?

Roughly map existing content to the 01–10 document model. You don't have to be exact yet—you're deciding which strategy fits.

Step 2: Choose Your Strategy

The pack supports three ways to clean up:

| Strategy | When to use | |----------|-------------| | Restructure | You want the full docs/01–10 structure. You archive existing docs (all at once or as you review), then impose the new structure and transfer content systematically. | | Migrate | You have existing docs and want to merge them into 01–10. You create the structure, then move or merge content into the right drafts. | | Review only | You want to keep your current folder structure. You use the pack's standards and checklists to review where docs lack—metadata, traceability, consistency—without creating docs/01–10. |

Pick one. Restructure and Migrate give you the full methodology; Review only improves what you have in place.

Step 3: Install the Pack and Run Compile

Download the pack (ZIP or via the context CLI). Install using your chosen flavour—for review only, run the installer with --install-option Flavour=ReviewOnly so it does not create docs/01–10. For restructure or migrate, use the default (full) install so docs/01–10 and draft templates are created.

After install, run ctx compile --pack pack-01-documentation-management from the repo root. That builds AI context (Cursor rules, skills, CLAUDE.md) so your AI has the methodology.

Step 4: Work in Methodology Order

For restructure or migrate: work in order 01 → 02 → … → 05, then 06–10 as needed. Use each draft's Methodology section to guide you. Preserve traceability (02→03→05→08). For review only: work through the checklists on your existing docs—general document, metadata, tools/assets, traceability.

Done when: Docs live in the 01–10 structure (or your structure is improved per checklists), content matches document standards, traceability is maintained, and there are no major stray or misleading docs left.

Conclusion

Cleaning up messy documentation is a matter of assess → choose strategy → install → work in order. The Documentation Management Pack gives you the checklists and the methodology so you know exactly what to do and when you're done.

Get the pack. Run the guide.