• accumulate project knowledge that compounds over time instead of scattering across tools
• keep clinical observations, user interviews, literature, and competitive intelligence organized and cross-referenced
• maintain a living evidence base that updates as new information arrives
• give new team members a structured way to get up to speed on a project

• "What is the project about? What problem are you working on?"
• "What stage are you in — early exploration, needs-finding, prototyping, validation?"
• "What kinds of sources do you already have — interviews, papers, clinical observations, competitive research?"

AGENTS.md

CLAUDE.md

• If one exists: append a clearly scoped

  ## Project Wiki Schema

  section to the existing file. Do not overwrite or remove any existing content — the file may contain instructions for other tools or skills.
• If neither exists: create a new

  AGENTS.md

  at the project root.

• the wiki directory structure and conventions
• the project domain and key terminology
• page naming conventions
• how to handle ingestion, queries, and maintenance
• which Biodesign stage the project is in and what that means for page priorities
• cross-referencing conventions (use standard Markdown links)

• paste text directly into the conversation
• share or upload a file (PDF, image, markdown, transcript)
• share a URL
• dictate or describe an observation

1. Save the source — classify the source type (interview, paper, observation, competitor, regulatory) and save it to the correct

   wiki/raw/

   subfolder with a descriptive, dated filename. The user never needs to navigate the folder structure manually.
2. Read the source completely
3. Discuss key takeaways with the user — what surprised them, what confirms existing thinking, what challenges it
4. Write or update a summary page in the wiki
5. Update

   wiki/pages/index.md

6. Update every relevant entity, concept, and evidence page across the wiki
7. Flag contradictions with existing wiki content explicitly — do not silently overwrite
8. Append an entry to

   wiki/pages/log.md

1. Read

   wiki/pages/index.md

   to find relevant pages
2. Read those pages and synthesize an answer with citations to specific wiki pages and raw sources
3. If the answer reveals a useful synthesis, comparison, or connection — offer to file it as a new wiki page so it compounds rather than disappearing into chat history

• Contradictions — pages that disagree with each other or with newer sources
• Stale claims — assertions that newer evidence has superseded
• Orphan pages — pages with no inbound links from other pages
• Missing pages — important concepts mentioned on other pages but lacking their own page
• Missing cross-references — pages that should link to each other but don't
• Evidence gaps — questions or claims that lack supporting sources
• Stage alignment — whether the wiki's depth matches the project's current Biodesign stage

• who they are
• how the problem affects them
• their role in adoption decisions (decision-maker, influencer, user, payer)
• evidence from interviews or observations
• links to relevant raw sources

• clinical evidence for the problem
• current standard of care and its limitations
• quantitative burden (prevalence, cost, outcomes data)
• key studies and their findings

• existing solutions and their strengths and limitations
• adjacent technologies
• market size and dynamics
• IP considerations

• user journeys and workflows
• data model choices
• architecture decisions and rationale
• implementation milestones

• applicable regulations and standards
• classification decisions
• submission pathway
• open regulatory questions

build-an-app

"Your planning documents are ready. Would you like to set up a project wiki to keep accumulating knowledge as you build? The wiki will seed from your planning docs and grow as you add interviews, papers, and clinical observations."

• Raw sources are immutable. Never modify anything in

  wiki/raw/

  . The AI reads from raw sources but only writes to

  wiki/pages/

  .
• Flag contradictions, don't hide them. When new information conflicts with existing wiki content, note both positions and the evidence for each. Let the user decide what to believe.
• Cite everything. Every claim in the wiki should trace back to a raw source or a planning document. Use Markdown links.
• Keep pages concise. A wiki page should be readable in 2–3 minutes. Split long pages into focused sub-pages.
• Don't fabricate evidence. If the wiki has gaps, say so. Add the gap to

  questions/open-questions.md

  rather than filling it with speculation.
• Respect the user's domain expertise. The AI maintains the wiki; the user directs the analysis. Ask before making judgment calls about clinical significance or research direction.
• The wiki is a git repo. Encourage commits after significant updates. The version history is valuable.

• Project scope and stage understood
• Directory structure created
• Existing planning docs seeded into wiki
• Schema file (AGENTS.md or CLAUDE.md) written and tailored to the project
• Index and log files initialized
• At least one source ingested interactively to demonstrate the workflow
• User understands ingest, query, and lint workflows