Agent skill

Compile Knowledge

by flonat in flonat/flonat-research

Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki.

MITAuto-check passedProductivity & Automation

Install Compile Knowledge

skills CLI
$ npx skills add flonat/flonat-research --skill compile-knowledge -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install flonat/flonat-research compile-knowledge --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/compile-knowledge .claude/skills/compile-knowledge && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
compile-knowledge
GitHub stars
145
Token cost
~2.5k tokens
SKILL.md length
921 words
Files
1
Skills in repo
83
Repo updated
First seen
Licence
MIT

At a glance

Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki.

  • Works in 6 steps: Locate Project and Scan Sources → Identify Concepts → Compile Articles → …
  • Project evidence is scattered across source records and needs synthesis into durable articles
  • SKILL.md covers When to Use, When NOT to Use, Architecture and Modes, plus 8 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Compile Knowledge is an agent skill from flonat/flonat-research. Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki. Use when project evidence is scattered across source records and needs synthesis into durable articles. Not for promoting existing articles into the global vault wiki; use $wiki-grow.

Its SKILL.md is about 2.5k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Productivity & Automation, covering Meeting notes and agendas. The repository describes itself as: Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows. The licence is MIT.

When your agent uses it

  • Project evidence is scattered across source records and needs synthesis into durable articles
  • Tasks that involve Meeting notes and agendas

Example prompts

  • “/compile-knowledge”

Requirements

  • Pre-approved tools (allowed-tools): Read, Glob, Grep, Write, Edit, Bash(mkdir*), Agent

Workflow steps

6 steps, taken from the step headings in SKILL.md.

  1. Locate Project and Scan Sources
  2. Identify Concepts
  3. Compile Articles
  4. Update Index
  5. Atlas frontmatter sync
  6. Incremental Mode

What it can do on your machine

Read from SKILL.md and the folder at commit da27600. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Glob
    • Grep
    • Write
    • Edit
    • Bash(mkdir*)
    • Agent

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Compile Knowledge loads about 2.5k tokens when it runs. Until then it costs about 79 tokens; SKILL.md has 921 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~79
When it runs · the whole SKILL.md, loaded when a task matches
~2.5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from flonat/flonat-research at commit da27600, republished under its MIT licence (© flonat). 921 words, ~2,530 tokens.

Download SKILL.mdSave it as .claude/skills/compile-knowledge/SKILL.md (or your agent's skills folder).
name
compile-knowledge
description
Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki. Use when project evidence is scattered across source records and needs synthesis into durable articles. Not for promoting existing articles into the global vault wiki; use $wiki-grow.
allowed-tools
Read, Glob, Grep, Write, Edit, Bash(mkdir*), Agent
argument-hint
[project-path] [--autonomous|-y] (no args = CWD)

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

ModeInvocationBehaviour
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.
Autonomouscompile-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 pointDefault
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 1Skip remaining phases; emit No sources to compile. and exit clean.
Concept granularity uncertainPrefer 400-600 word articles, specific scope over generic. Err on the side of fewer, sharper concepts.
Article exists but scope shiftedUpdate in place when overlap ≥50% with new finding; create new article only when genuinely orthogonal.
Contradictions between sourcesFlag 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 >1Skip silently (already documented in Phase 5.4).
Article exceeds 1000 wordsSplit 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:
SourceLocationWhat to extract
Literature reviewsdocs/literature-review/Paper summaries, key findings, research gaps
Meeting notesmeeting-notes/ or to-sort/ recapsDecisions, insights, action items
Session logslog/Research progress, discoveries, pivots
MEMORY.mdProject rootNotation, decisions, pitfalls, domain corrections
Atlas topic file~/vault/atlas/<theme>/<slug>.mdStatus, connected topics, research questions
Code README/commentscode/, src/What the code does, key algorithms
Paper sectionspaper-*/paper/*.texCurrent argument structure, contributions
.context/project-recap.md.context/Project overview, current state
  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/
Show full SKILL.md (382 more words)Show less

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:

markdown
# <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:

markdown
# 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

SkillRelationship
store-insightLightweight single-finding filer — called by other skills
knowledge-lintChecks compiled knowledge for inconsistencies
literature (pipeline mode)Produces literature reviews that feed into compilation
session-closeExtracts session insights and files them via store-insight

© flonat, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/compile-knowledge of flonat/flonat-research.

Open the folder on GitHubat commit da27600

Compare with similar skills

Compile Knowledge next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Compile Knowledge compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Compile Knowledge this skillflonat/flonat-research145—~2.5kAutomated safety check: PassMIT
Daily Journalravila4/claude-adhd-skills157—~2.5kAutomated safety check: PassMIT
GranolaArtemXTech/claude-code-obsidian-starter224—~905Automated safety check: PassNone
Ingestcoreyhaines31/makerskills848—~1.8kAutomated safety check: PassMIT
Paperclip Distillpaperclipai/paperclip99k—~2.8kAutomated safety check: PassMIT
Meeting SummarySourceWeft/SourceWeft166—~197Automated safety check: PassCustom licence

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Questions about Compile Knowledge

What does Compile Knowledge do?

Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki. Compile Knowledge is an agent skill from flonat/flonat-research. Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki.

When should I use Compile Knowledge?

Compile Knowledge fits situations like: project evidence is scattered across source records and needs synthesis into durable articles; tasks that involve Meeting notes and agendas.

How do I install Compile Knowledge in Claude Code?

Run `npx skills add flonat/flonat-research --skill compile-knowledge -a claude-code`. Or copy the skill folder (skills/compile-knowledge in flonat/flonat-research) into .claude/skills/compile-knowledge in your project. Claude Code loads it when a task matches its description.

How do I install Compile Knowledge in Codex?

Run `npx skills add flonat/flonat-research --skill compile-knowledge -a codex`. Or copy the skill folder (skills/compile-knowledge in flonat/flonat-research) into .agents/skills/compile-knowledge in your project. Codex loads it when a task matches its description.

Can I use Compile Knowledge in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add flonat/flonat-research --skill compile-knowledge -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/compile-knowledge, .gemini/skills/compile-knowledge, .github/skills/compile-knowledge and .opencode/skills/compile-knowledge in your project.

What does Compile Knowledge need to run?

SKILL.md names no scripts, command-line tools or credentials: Compile Knowledge is instructions for the agent only. Its frontmatter pre-approves these tools: Read, Glob, Grep, Write, Edit, Bash(mkdir*), Agent.

Does Compile Knowledge access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Compile Knowledge safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Compile Knowledge use?

Compile Knowledge is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Compile Knowledge use?

About 2.5k tokens (SKILL.md is roughly 10k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Compile Knowledge?

Skills that share tags, products or a category with Compile Knowledge: Daily Journal (ravila4/claude-adhd-skills, 157 stars), Granola (ArtemXTech/claude-code-obsidian-starter, 224 stars), Ingest (coreyhaines31/makerskills, 848 stars) and Paperclip Distill (paperclipai/paperclip, 99k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Compile Knowledge?

flonat (a GitHub user) maintains it in flonat/flonat-research, which has 145 GitHub stars. The repository holds 83 skills in this directory. The repository was last updated on September 29, 2026.

Source: flonat/flonat-research on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.