Librarian Vault Manager

Overview

This skill provides the foundational knowledge and rules for managing Obsidian vaults structured using the Johnny-Decimal and Zettelkasten methodologies, enhanced with graph-aware metadata for advanced RAG systems.

Core Mandates

Graph-Aware Metadata: CRITICAL. Every permanent note MUST include YAML frontmatter with required core fields entities, communities, and status. Add aliases and tags when they improve discoverability or actionable intent.
Read-Only Analysis and Proposals: NEVER create, modify, or delete files directly without a preceding proposal phase.
Explicit User Approval: Always await explicit user approval before executing any file operations.
Respect ACID Notation: All references must strictly follow the SYS.AC.ID format (Area, Category, ID).
Adherence to Vault Guidelines: Consult references/librarian/copilot-instructions.md for identity, atomicity, titles, and links.
Maintain JDex Integrity: 00.00.md index and _SYS/*.base configuration must be kept consistent.

System Knowledge

Graph-RAG Hybrid: A methodology where structured frontmatter (entities, communities) is injected into the text for embedding, enabling "graph-aware" semantic search.
Johnny Decimal: Hierarchical organization (Area -> Category -> ID). 00 is reserved for indices.
Zettelkasten: Atomic, evergreen notes that evolve from transient observations to durable knowledge.
Agent Memory (AGNT): A specialized system for Procedural Memory (Rules in AGNT/) and Episodic Memory (Logs in JRNL/AGNT/). The AGNT system is strictly for agent procedural rules, coding standards, and user preferences. It MUST remain entirely isolated from the user's personal knowledge domains (LIFE, WORK, etc.). An agent must never store facts about the world in AGNT, and must never store rules about how to act in the user's personal domains. Procedural rules use strict JD ACID notation and declarative titles.
Journal System (JRNL): The JRNL/ system (including JRNL/AGNT/) is the transient scratchpad and Episodic Memory. While indexed by the RAG database for historical context and recall, its contents must never be treated as authoritative, crystallized knowledge. If a RAG query returns a conflict between a JRNL note and an evergreen SYS.AC.ID note, the evergreen note always takes precedence.

MCP Backend

Vault reads and writes go through the obsidian-vault-mcp MCP server (jabez007/obsidian-vault-mcp, v2+). Two behaviors matter when proposing changes:

obsidian_create_note and obsidian_move_note refuse to overwrite an existing file unless overwrite: true is passed. Treat a refusal as an ACID ID collision to resolve, not an error to force past.
Note-writing tools re-index the changed note inside the server, so no separate re-index step is needed after a write.

Mandatory YAML Schema

Every note must start with YAML frontmatter whose required core fields are:

---
entities: [<entity-1>, <entity-2>, <entity-3>]
communities: [<jd-category-or-cluster>]
status: distilled
---

Allowed values: distilled, crystallized, synthesized, scaffolded.

Replace every <token> before writing a note. entities and communities are exact-match filter keys, so placeholder text becomes an unusable graph label.

aliases and tags may also be included when they add useful synonyms or actionable intent.

Librarian Specialists (Subagents)

For complex workflows, delegate to these specialized subagents:

@librarian: General vault questions, ID lookups, and coordination.
@vault-auditor: Audit link health, identify orphans, and suggest connections.
@vault-cleaner: Maintain hygiene, detect duplicates, and fix naming issues.
@vault-synthesizer: Identify contradictions, synergies, and gaps; propose synthesis notes.
@vault-scaffolder: Create new systems, areas, or categories from scratch.
@daily-reviewer: Extract durable knowledge and recurring themes from daily logs.
@source-distiller: Process long-form content (articles, transcripts) into atomic notes.
@flashcard-generator: Automatically create study materials from notes.

General Reference Documents

Johnny Decimal System: references/librarian/johnny-decimal.md
Zettelkasten Method: references/librarian/zettelkasten.md
Vault Philosophy: references/librarian/philosophy.md
Copilot Instructions: references/librarian/copilot-instructions.md

librarian-vault-manager

SKILL.md.gemini/skills/librarian-vault-manager/SKILL.md