| name | vault-system |
| description | Use when maintaining the vault ITSELF as a system, not its content: knowledge-graph build/rebuild/query (graphify), second-brain mapping, vault diagnose/audit/hygiene, drift detection, extract rules from vault, backfill journals, setup vault types, consolidate memory (index over cap), Obsidian tooling (CLI/Bases/Markdown/JSON Canvas), vault bloat or Obsidian slow. Answering questions FROM the graph, use graph-query tools; daily journal/coaching/pattern detection, use those skills. |
| trigger | /vault-system |
Vault system
Routes vault meta-maintenance — the vault AS a system (its markdown corpus, knowledge graph, drift monitors, rule extraction, substrate sync). Not the content; the substrate that makes the content queryable and auditable.
Distinct from:
- Querying the vault to answer a question (use the knowledge-graph query tools)
- Bringing external data INTO the vault (use the ingest skills)
- Daily journal + coaching + pattern detection (those operate inside the substrate)
This is the SUBSTRATE layer. It maintains what every other skill uses.
Step 1. Identify the maintenance moment
| Trigger | Skill / tool |
|---|
| Knowledge graph stale or never built for a corpus | graphify |
| Existing graph query (find concept / path / cluster) | your graph-query tool, or Obsidian graph view |
| Typed-file metadata extraction (books, meetings, people, articles, goals) | second-brain-mapping |
| Vault self-check (CLAUDE.md / Meta folder / skills / hooks / MCPs / journal index) | diagnose |
| Files edited many times in a short window (drift hotspot) | a drift-detection pass → a Drift Audit note |
| Recurring corruption pattern needs codification | codify it into a new rule file in your rules dir |
| Journals missing body / frontmatter context | backfill-journal-body-context |
| Vault types not yet set up (new vault or refresh) | setup-vault-types |
| Memory index getting long (truncation cliff) | consolidate-memory |
| Obsidian Bases / JSON Canvas / Markdown / CLI work | the matching obsidian:* skill |
If unclear → ask ONE question. Don't guess.
Step 2. Pre-flight
- Vault location: resolve the vault root (a
VAULT_PATH / VAULT_ROOT env var, or the current directory).
- Graph state: check whether a graph report exists and how fresh it is before answering graph questions.
- Drift state: check the latest drift-audit output.
- Rules state: list the rules directory.
- Memory state: check the memory index length (keep it under the truncation cliff).
- Git in a large vault: NEVER
git add -A / . / unscoped git status on a big vault — full-tree walks are slow and lock-contending. Use explicit paths.
Step 3. Route by work-type
Knowledge graph
- Build a new graph from a corpus (code / docs / papers / images) →
graphify
- Query an existing graph (search nodes / neighbors / path) → your graph-query tool
- Coverage audit (which corpus chunks were processed) → graphify's coverage audit
Second-brain mapping
- Extract structured metadata from every typed file →
second-brain-mapping
- Apply wikilinks from detected entities →
second-brain-mapping (wikilink phase)
- Cross-type insights (patterns no single file shows) →
second-brain-mapping (insights phase)
Diagnostics + drift
- Vault self-check →
diagnose
- Drift detection (files edited many times in 30d) → a drift-detection pass → a Drift Audit note
Rule extraction + memory
- Extract recurring patterns into a CLAUDE.md rule / rules file → codify manually into a new rule file
- Consolidate memory files (merge duplicates, prune the index) →
consolidate-memory
Journal hygiene
- Backfill journal body / frontmatter context →
backfill-journal-body-context
- Tag / taxonomy consistency check → manual against your canonical tag list
Vault setup + onboarding
- Setup vault types (frontmatter taxonomy) →
setup-vault-types
- Setup the substrate on a new vault → the bootstrap flow
Obsidian tooling
- CLI (backlinks, search, unresolved, orphans, properties) →
obsidian:obsidian-cli
- Bases queries (typed views) →
obsidian:obsidian-bases
- JSON Canvas creation / edit →
obsidian:json-canvas
- Markdown specifics (callouts, wikilinks, embeds) →
obsidian:obsidian-markdown
Step 4. Post-flight (gates "done")
- Graph rebuilt + report regenerated if graphify ran.
- Memory index under the truncation cliff post-consolidation.
- Drift hotspots resolved if the Drift Audit surfaced any.
- New rules indexed in the rules directory.
- Vault committed with explicit paths (never raw
git add -A in a large vault).
Common mistakes
git add -A in a large vault. Long walks + lock contention. Use explicit paths.- Editing aggregator outputs directly (e.g. a "Last Session" or "Decision Log" roll-up). Edit the per-entry source files; let the aggregator rebuild.
- Hand-editing symlinked skill copies. Edit the source repo + re-sync.
- Re-reading the memory index when it is already in context.
- Routing daily journal / coaching / pattern detection here. Those are their own skills; this umbrella maintains the substrate, not the content.
