compile-knowledge

name	compile-knowledge
description	Use when you need to compile raw inputs (literature, meeting notes, session logs, code findings) into a per-project knowledge wiki. Supports --autonomous / -y for end-to-end runs without prompts (used by the Saturday wiki-grow cron).
allowed-tools	Read, Glob, Grep, Write, Edit, Bash(mkdir*), Agent
argument-hint	[project-path] [--autonomous|-y] (no args = CWD)
skill-dependencies	["audit-project-research"]

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 audit-project-research
• 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

Mode	Invocation	Behaviour
Interactive (default)	compile-knowledge [project-path]	Phases run normally; mid-run nudges allowed where useful; end-of-run summary requires no confirmation but the user can inspect output and re-run.
Autonomous	compile-knowledge [project-path] --autonomous (or -y)	End-to-end run with zero prompts. All decisions take the documented default. Single end-of-run summary is the only user-facing output. Used by the Saturday wiki-grow cron to refresh project knowledge before the wiki-promotion pass.

Autonomous-mode defaults (every choice point)

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

Choice point	Default
Project path unresolved (CWD not a research project)	Fail with a single one-line error to stderr. Do not prompt for path.
No sources found in Phase 1	Skip remaining phases; emit No sources to compile. and exit clean.
Concept granularity uncertain	Prefer 400-600 word articles, specific scope over generic. Err on the side of fewer, sharper concepts.
Article exists but scope shifted	Update in place when overlap ≥50% with new finding; create new article only when genuinely orthogonal.
Contradictions between sources	Flag explicitly in prose ("Source A says X, Source B says Y") — never silently pick a side.
Source can't be parsed (encoding, malformed)	Log to the Gaps section in _index.md; continue with remaining sources.
Atlas topic match in Phase 5 is 0 or >1	Skip silently (already documented in Phase 5.4).
Article exceeds 1000 words	Split into two articles by sub-theme; never truncate findings.

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:

Source	Location	What to extract
Literature reviews	docs/literature-review/	Paper summaries, key findings, research gaps
Meeting notes	meeting-notes/ or to-sort/ recaps	Decisions, insights, action items
Session logs	log/	Research progress, discoveries, pivots
MEMORY.md	Project root	Notation, decisions, pitfalls, domain corrections
Atlas topic file	~/vault/atlas/<theme>/<slug>.md	Status, connected topics, research questions
Code README/comments	code/, src/	What the code does, key algorithms
Paper sections	paper-*/paper/*.tex	Current argument structure, contributions
.context/project-recap.md	.context/	Project overview, current state

3. 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).
3. If the field already exists, overwrite. If absent, insert before the closing ---.
4. 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

Skill	Relationship
store-insight	Lightweight single-finding filer — called by other skills
knowledge-lint	Checks compiled knowledge for inconsistencies
literature (pipeline mode)	Produces literature reviews that feed into compilation
session-close	Extracts session insights and files them via store-insight