The Three-Layer Architecture

The three-layer architecture is the safety boundary of an LLM Wiki. Do not let the agent freely edit original sources, and do not hide operating rules inside vague chat prompts.

Layer 1: immutable raw sources

raw/ holds originals: PDFs, markdown exports, transcripts, screenshots, CSVs, meeting notes, and clipped web pages. The agent may read this directory, but it should not modify or delete it. If a bad synthesis happens, the raw layer lets you rebuild the wiki from preserved evidence.

Layer 2: dynamic compiled wiki

wiki/ is the mutable output. It contains concept pages, source summaries, entity pages, syntheses, contradictions, and open questions. The agent may update this layer during ingest, query, and lint operations.

Layer 3: algorithmic schema

AGENTS.md, CLAUDE.md, or an equivalent root instruction file is the operating contract. It tells the agent which directories exist, which files are read-only, how pages are shaped, how links are written, and which checklist must be completed before a task is done.

Layer	Write access	Primary job	Failure if mixed
raw/	Human and import tools only	Preserve ground truth	AI edits can destroy the evidence needed to recover.
wiki/	Agent may edit under schema rules	Maintain synthesized knowledge	The graph becomes a pile of notes with no predictable shape.
AGENTS.md	Human-reviewed edits	Define agent behavior	The model improvises file paths, metadata, and safety rules.

Recommended folder tree

raw/
  papers/
  web/
  meetings/
  attachments/

wiki/
  index.md
  log.md
  concepts/
  entities/
  sources/
  syntheses/
  contradictions.md
  open-questions.md

AGENTS.md

Permission checklist

Raw files are read-only during agent operations.
Every compiled page has frontmatter, source status, and related links.
Every ingest updates wiki/index.md and wiki/log.md.
Every contradiction is preserved until a human resolves it.
Every destructive cleanup requires explicit human approval.