llm-wiki

LLM Wiki: Agent SOP

This is the main "Operating Manual" for the LLM Wiki project. It manages the lifecycle of knowledge: Ingest → Query → Lint → Graph.

🧭 Core Workflow Index

For detailed instructions, refer to the specialized reference files.

Stage	Action	Reference
Ingest	`/wiki-ingest [<file>\|--from <dir>]`	`references/ingest-advanced.md`
Query	`/wiki-query <question>`	`references/query-advanced.md`
Save	`/wiki-synthesize [slug]`	`SKILL.md#wiki-synthesize`
Maintain	`/wiki-lint` \| `/wiki-graph`	`SKILL.md#maintenance`
Edit	`/wiki-update` \| `/wiki-delete`	`SKILL.md#lifecycle`
Ontology	`/wiki-ontology-*`	`references/ontology-commands.md`

🏗️ Project Layout

wiki/
  index.md          # Catalog of all pages (Update EVERY ingest)
  log.md            # Chronological record (Append-only)
  history.json      # Ingest registry (Always use Write tool)
  sources/          # Summaries (kebab-case.md)
  entities/         # People/Projects (TitleCase.md)
  concepts/         # Ideas/Theories (TitleCase.md)
  syntheses/        # Saved query answers
  originals/        # Read-only archive
  ontologies/       # (OPTIONAL) Structured YAML data

Templates & Schema → references/templates.md | Wikilinks: [[PageName]] (Case-Sensitive)

📥 Ingest Process

Main Goal: Transform raw input into structured wiki pages and archive the original.

Analysis: Read source. Determine title/slug.
Strategy: Select mode (Full vs. Summary-Only).
- Summary-Only: .xlsx, .pptx, .pdf > 30p, or --summary-only flag.
Execution:
- Write wiki/sources/<slug>.md.
- Update wiki/index.md using hierarchical categorization (e.g., Hobby/Cycling) — see references/ingest-advanced.md for rules and defaults.
- Create/Update wiki/entities/ and wiki/concepts/.
Registration: Update wiki/history.json and append to wiki/log.md.

Advanced flags (--to, --precision, --no-interview, etc.) → references/ingest-advanced.md

🔍 Query & Synthesis

/wiki-query

Discover relevant pages from wiki/index.md, wiki/synthesis-map.md, and wiki-hub.md.
Gather context from sources/, entities/, concepts/, and ontologies/. If a file is in wiki-hub.md, cite the external source repo.
Synthesize answer with [[PageName]] citations. Structural filters (class:, type:, AND/OR) → references/query-advanced.md

/wiki-synthesize

Saves the last query answer to wiki/syntheses/<slug>.md.

Generate slug from question.
Update wiki/synthesis-map.md (append-only) and wiki/log.md.

🛠️ Maintenance & Lifecycle

#maintenance

/wiki-lint: Check orphans, broken links, stale summaries. (Report: wiki/lint-report.md). If wiki-hub.md exists, ignore/lower severity of broken links originating from imported external files.
/wiki-graph: Rebuild graph/graph.json and graph/graph.html.

#lifecycle

/wiki-sources: List ingested sources from history.json.
/wiki-update : Refresh a source from its original file.
/wiki-delete : Soft-delete source (keep in history, remove pages).

🔗 Wiki-Hub Architecture Support

When a wiki-hub.md file exists at the project root, it acts as the authoritative registry for external files.

1. External Source Citation

During /wiki-query, the agent MUST check wiki-hub.md for any file used in the answer.
If the file is listed as an imported source, the citation should include the external repository information (e.g., [[PageName]] (Source: repo-name)).

2. Linting Exceptions

/wiki-lint should read the ## Imported Sources list in wiki-hub.md.
Broken link warnings for files listed in the hub should be suppressed or marked as "External" to avoid unnecessary noise from links pointing to non-imported dependencies.

3. File Integrity

Do not overwrite, modify, or delete files tracked in wiki-hub.md without explicit user confirmation. These files are managed externally via the hub.

⚠️ Gotchas & Critical Rules

READ-ONLY: Never modify wiki/originals/.
CONSISTENCY: wiki/index.md must be updated on every ingest to keep query discovery working.
HISTORY: Always read-merge-write wiki/history.json.
CLEANUP: When deleting, check for orphaned entity/concept pages.