The hub (~/wiki/) is just a registry. No content — only wikis.json, _index.md, and log.md. All content lives in topic sub-wikis.
Topic wikis (~/wiki/topics/<name>/) are isolated research areas. Each has its own sources, articles, outputs, and Obsidian vault config. Isolation means researching quantum computing can't pollute your nutrition wiki.
Raw sources (raw/) are immutable. Once a paper, article, or data file is ingested, it's never modified. This is the audit trail — every claim in every article traces back to a source.
Wiki articles (wiki/) are LLM-compiled syntheses organized into three categories:
- Concepts — foundational ideas, mechanisms, theories
- Topics — specific subjects, comparisons, state-of-the-field
- References — tools, frameworks, data tables, lookup resources
Archive (topics/.archive/) is for whole topic wikis the user no longer wants in normal context. It preserves source history, articles, outputs, and logs while keeping old interests quiet by default.
Sessions (HUB/.sessions/) are operational memory for redacted harness checkpoints, compact digests, rehydration indexes, and feedback candidates. They are not compiled as topic evidence unless explicitly promoted into raw/notes/.
Inventory (inventory/) is for durable operational state: actual items, source candidates, corpora, entities, open questions, tasks, watch items, and next actions. It is intentionally not evidence for factual claims.
Dataset manifests (datasets/) let the wiki index large or external data without copying it into raw/. Manifests can point to local paths, URLs, archives, samples, profiles, and query recipes.
Articles use dual-link format: [[wikilink]] for Obsidian + standard markdown links for everything else. Confidence scores (high/medium/low) reflect source quality and corroboration.
Indexes (_index.md) exist in every directory. They're derived caches — rebuilt automatically from file frontmatter. The agent reads indexes first and never scans blindly.
Outputs (output/) are generated artifacts: reports, slide outlines, study guides, implementation plans. They're built from wiki articles, so every output compounds on all prior research.
Audit walks that full artifact graph. It can trace an output back through the wiki state and raw sources it depended on, then escalate into fresh research when the stored evidence is stale or incomplete.