flonat/flonat-research/compile-knowledge

Compile Knowledge

Reads raw inputs from a project and compiles/updates a knowledge/ wiki — a collection of LLM-maintained markdown articles that synthesise everything known about the project's domain.

When to Use

• After a literature review to consolidate findings
• After a series of sessions on a project to build up the knowledge base
• When starting work on a project and wanting to understand the state of knowledge
• Periodically to keep the knowledge wiki fresh

When NOT to Use

• For structural project audits — use an installed research-project audit workflow
• For atlas topic metadata — that stays in the vault
• For session-specific notes — those go in log/

Architecture

The knowledge wiki lives at <project>/knowledge/:

knowledge/
  _index.md          ← auto-maintained index with brief summaries
  concept-name.md    ← one article per concept
  concept-name-2.md

The LLM owns this directory. the user rarely edits it directly. The value is in the compilation — connecting dots across sources that no single document contains.

Modes

Autonomous-mode defaults (every choice point)

When --autonomous / -y is set, the skill takes these defaults silently:

Autonomous-mode does NOT change

• Knowledge-article quality contract: every claim must cite its source. Unverifiable claims get [UNVERIFIED] per the global rule.
• Phase 5 atlas frontmatter sync: still writes knowledge_last_compiled on every run.
• Read-only access to data/raw/ per the global data-sensitivity rule.
• Per-project MEMORY.md / CLAUDE.md are NEVER edited by this skill.

If any of the above fails (e.g. an [UNVERIFIED] flag couldn't be applied due to a write error), include the failure in the end-of-run summary rather than blocking.

Phase 1: Locate Project and Scan Sources

1. Resolve project path (CWD or argument)
2. Scan for raw inputs:

1. Report source inventory:

`` Sources found: Literature: 12 papers in docs/literature-review/ Sessions: 8 logs in log/ Memory: 14 entries in MEMORY.md Paper: 3 sections drafted Code: 2 scripts in code/python/ ``

Phase 2: Identify Concepts

Read all sources and extract a concept list — the key ideas, methods, datasets, theories, and phenomena that the project deals with.

Concept granularity: Each concept should be specific enough to warrant its own article (~200-1000 words). Too broad = useless summary. Too narrow = fragmented.

Examples of good concepts:

• mechanism-design-for-audits.md (a specific method applied to the project's domain)
• collusion-detection-methods.md (a family of techniques relevant to the project)
• eu-ets-carbon-market.md (institutional context)
• callaway-santanna-estimator.md (a specific estimator used)

Examples of bad concepts:

• introduction.md (too structural — that's the paper's job)
• regression.md (too generic)
• table-3.md (too narrow)

Phase 3: Compile Articles

For each concept, create or update knowledge/<concept-name>.md:

# <Concept Name>
 
> One-sentence summary of what this concept is and why it matters to the project.
 
## Key Findings
 
-Bullet points synthesising what is known from all sources
-Each finding should cite its source: (Author Year) or (session log YYYY-MM-DD)
-Flag contradictions: "Source A says X, but Source B says Y"
 
## Open Questions
 
-What is not yet known or resolved
-Questions that emerged from the literature but aren't answered
-Methodological choices that remain open
 
## Sources
 
| Source | Type | Key contribution |
|--------|------|-----------------|
| Author (Year) | Paper | Finding X |
| Session 2026-03-15 | Log | Discovered Y |
| MEMORY.md | Decision | Chose Z because... |
 
## Related
 
-[[other-concept]] — how they connect
-Atlas: `<topic-slug>` — link to atlas topic if relevant

Rules:

• Be specific and factual — no filler prose
• Cite sources for every claim
• Flag contradictions explicitly rather than silently picking one side
• Keep articles between 200-1000 words
• Use [[wikilink]] syntax for cross-references between knowledge articles

Phase 4: Update Index

Write or update knowledge/_index.md:

# Knowledge Index
 
> Auto-maintained by `compile-knowledge`. Last updated: YYYY-MM-DD.
> N articles, ~X words total.
 
## Articles
 
| Article | Summary | Sources | Last updated |
|---------|---------|---------|-------------|
| [Concept A](concept-a.md) | One-line summary | 3 papers, 2 sessions | YYYY-MM-DD |
| [Concept B](concept-b.md) | One-line summary | 1 paper, 1 decision | YYYY-MM-DD |
 
## Source Coverage
 
| Source type | Count | Compiled into articles |
|------------|-------|----------------------|
| Papers | 12 | 10 (2 not yet compiled) |
| Session logs | 8 | 5 (3 not yet compiled) |
| Memory entries | 14 | 12 |
 
## Gaps
 
-[List concepts that should exist but don't yet]
-[Sources not yet compiled into any article]

Phase 5: Atlas frontmatter sync

After writing _index.md, also update the atlas topic frontmatter so the project's compile date is discoverable from outside the project (e.g. by session-close, the wiki promotion cron, atlas-workspace).

1. Resolve the atlas topic: grep -rl "project_path:.*$(basename "$PWD")" ~/vault/atlas/
2. If a single match is found, set or update the frontmatter field

knowledge_last_compiled: YYYY-MM-DD (today's date in UTC).

1. If the field already exists, overwrite. If absent, insert before the

closing ---.

1. If 0 or >1 atlas topic files match, skip silently and log to the

end-of-run summary (Atlas frontmatter sync: skipped — N matches).

The field is consumed by:

• session-close (info-only freshness line via

references/research-checks.md § 18)

• The Saturday wiki-grow cron (uses the date to schedule re-promotion)
• atlas-workspace (could surface in topic-page metadata row in future)

Phase 6: Incremental Mode

When run on a project that already has knowledge/:

1. Detect new sources since last compilation (check _index.md last-updated date vs source file modification dates)
2. Only process new/modified sources
3. Update existing articles with new findings (append, don't rewrite)
4. Create new articles only for genuinely new concepts
5. Update _index.md
6. Update atlas frontmatter knowledge_last_compiled (Phase 5)

Report:

Knowledge updated:
  Articles updated: 3 (concept-a, concept-b, concept-c)
  Articles created: 1 (new-concept)
  Sources processed: 4 new since last compile
  Total: N articles, ~X words

Output

Print summary after compilation:

Knowledge compiled for <project-name>:
  Articles: N (M new, K updated)
  Total words: ~X
  Sources compiled: Y / Z total
  Gaps: [list any uncompiled sources]
  Index: knowledge/_index.md

Cross-References