Obsidian Vault Builder (general PKM, multi-vault aware)

Patterns for operating an Obsidian vault from Claude Code: capture pipelines, plugin selection, REST API integration, file-portability discipline, methodology choice. Multi-vault aware.

For academic study vault construction (course prep, lecture notes, mock exams, exam-ready content): the durable patterns from the deprecated obsidian-study-vault-builder skill have been folded into this skill. See references/academic-vault.md. The companion skill itself was removed via PR #6 and re-validated 2026-05-15 (over-triggered on exam-prep prompts; structurally misaligned with the interactive-practice approach in the exam-prep protocol, itself ablated 2026-08-28).

When to use

• User asks to add/edit/query content in an Obsidian vault
• User asks to install or configure Obsidian plugins
• User wants to integrate Claude Code with Obsidian via Local REST API or CLI
• User wants to automate ongoing capture/organization/retrieval
• User wants to design a PKM workflow
• User asks to build a course/exam/study vault (see references/academic-vault.md)

Checkpoint-based vault build (greenfield, large generation tasks)

When generating a vault from scratch or filling in many chapters/sections at once, never generate everything upfront. Use progressive validation:

1. First chapter / first section — then STOP
2. User review — approve format, structure, quality
3. Remaining chapters / sections — continue with validated pattern
4. Final QA pass — systematic verification per references/qa-checklist.md

Why this matters:

• Catches format issues before they multiply across 30+ files
• Validates approach matches user needs early
• Adjusts course when cheap (chapter 1) vs expensive (chapter 8)
• Prevents 5+ hours of rework

Approximate time budget for a typical academic course (10 chapters): chapter 1 ~30 min, review ~15 min, remaining ~90 min, QA ~30 min = ~2.5 hours vs 80+ hours manual. Pattern is greenfield-build universal; applies equally to paper/book/codebase-docs generation.

Multi-vault layout (when applicable)

Many PKM users run more than one vault: a personal/manual vault (off-limits to agents) plus a Claude-native vault (default agent target). When the user has both, default writes target the Claude-native vault unless they explicitly extend access to the personal one.

Specific paths and override env vars belong in the user's CLAUDE.md, not in this skill, so the skill stays portable. For strong off-limits enforcement on the personal vault, consider a structural enforcement hook at the agent boundary that blocks Write/Edit/Bash mutations targeting paths under the personal vault.

Foundation plugins (summary)

Install only what's needed; soft cap ~10 active plugins. Core set:

• Local REST API — base layer for Claude Code <-> vault interaction (loopback HTTPS + bearer token)
• Obsidian Git — auto-commit + push to private remote (real backup tier)
• Templater — automation foundation for templates/scripts
• Daily Notes (core) — daily scaffolding baseline
• Style Settings — theme customization without CSS
• QuickAdd — macros + capture pipelines
• Smart Connections (multilingual caveats apply) — passive sidebar discovery via local embeddings
• Bases (core) — replaces ~70% of Dataview use cases

Detailed plugin notes (Calendar/Periodic Notes status, Smart Connections multilingual swap, AI-layer plugin caveats): see references/plugins.md.

Claude Code <-> vault interaction patterns (summary)

Five patterns, ordered by complexity:

1. Read directly via filesystem (Read tool)
2. Vault search via obsidian.com CLI (index-aware)
3. Local REST API direct (curl)
4. Bases queries (dashboards)
5. External tool to embed (PNG/SVG for complex viz)

Per-pattern details + CLI mapping table + multi-vault notes: see references/interaction-patterns.md.

Diagram tool selection (summary)

Mermaid is default for universal compatibility. When it hits a limit, the alternatives table covers Excalidraw, Draw.io, PlantUML, D2, Pikchr, WaveDrom, Kroki, TikZ, Python+Matplotlib. Tool selection factors: concept complexity, precision, platform priority, editability, time, dynamic-vs-static, version control.

Full table + decision tree + selection factors: see references/diagrams.md.

File-format philosophy

Files are file-portable by definition (markdown, txt, universal formats). Apps are transient tools; data is permanent. Use any Obsidian feature freely (wikilinks, transclusions, callouts, highlights, comments, Dataview/Bases queries).

Caveat: don't let a Dataview/Bases query be the only home of a fact. The query result is Obsidian-only; the underlying notes are portable.

Methodology choice

Backup discipline

Obsidian Sync's 30-day version history is NOT backup. For real backup:

1. git init in vault root
2. .gitignore for .obsidian/workspace*, .obsidian/cache*, .obsidian/plugins/*/data.json (plugin credentials), .smart-env/, .trash/
3. Auto-commit on session close (or scheduled)
4. Push to a private remote (GitHub private repo, or self-hosted)
5. Periodic restore drill: clone the remote into a scratch dir, verify content matches expectation. A backup that has never been restored is hope, not backup.

Common rendering pitfalls (summary)

Recurring issues when generating markdown for an Obsidian vault: Mermaid node-label syntax, LaTeX pipes in tables, wiki-link vs markdown-link conventions, collapsible callouts for active-learning content, universal-features discipline (mobile + future-proofing), structural-consistency patterns 5-8 (navigation/objectives/TOC/cross-refs), systematic fix approach (grep all -> fix all -> re-grep -> document), and minor unicode/table/HTML-tag pitfalls.

Full content + diagnose+fix recipes + universal-vs-platform feature table: see references/rendering-pitfalls.md.

Anti-patterns

• Plugin bloat (>10 active without startup measurement)
• Structure paralysis (weeks reorganizing folders, zero notes written)
• MOC paralysis (empty MOCs created preemptively)
• Daily-Note-only vault (365 daily notes, zero permanent notes)
• Sync-only backup (Obsidian Sync history is NOT backup; use obsidian-git as second tier)
• Dataview/Bases query as the only home of a fact
• Disabling Restricted Mode without an obsidianpluginaudit.com check
• File-dropping plugins from GitHub releases without surfacing the trust escalation (bypasses both store review and BRAT vetting)
• Committing .obsidian/plugins/*/data.json to git (often contains plaintext credentials)
• Sending non-ASCII bodies via REST API PUT without explicit UTF-8 charset header (causes U+FFFD corruption)
• Recommending Smart Connections for multilingual content without first swapping to a multilingual embedding model

Asset organization

Two patterns are in active community use; neither has clear consensus as the "right" one:

• Per-project: <project>/assets/ for diagrams/images, <project>/code/ for samples. Relative paths (![[../assets/x.png]]) keep the project portable. Best for project-as-unit thinking and easy git submodule.
• Flat attachment folder: Obsidian's default; single attachments/ (or configured equivalent) at vault root, all paste-images go there. Best for cross-cutting reuse and simpler image-management.

Pick based on portability needs (per-project wins) vs cross-vault reuse (flat wins). Avoid absolute paths in either pattern.

For vaults that grow, the standard PKM structure scales:

vault/
  Projects/<project-name>/
    notes/
    assets/        # diagrams, images
    code/          # example code
  Resources/       # textbooks, papers, reference PDFs
  Daily-Notes/
  Templates/

Tag by concept rather than by location (#async-patterns not #nodejs-folder). Properties for metadata (status, created, tags). Bases queries for dynamic overviews on top of the static folder structure.

For academic-study vault scaffolds (different shape, 00-overview / 01-chapter / cross-chapter / mock-exams): see references/academic-vault.md.

When NOT to use Obsidian

• Team collaboration: Notion
• Daily journaling + outlining primary: Logseq
• Already in Emacs: Org-mode/Org-roam
• Mac with heavy PDF workflow: DEVONthink + Obsidian split
• VS Code minimal-tooling: Foam/Dendron
• Spatial-narrative thinking: Tinderbox

Additional resources

Reference files

For detailed content beyond the summaries above:

• `references/plugins.md` — Foundation plugins, AI-layer plugins (caveats), Smart Connections multilingual swap
• `references/interaction-patterns.md` — Patterns 1-5 in detail + Manual-vs-CLI mapping table
• `references/diagrams.md` — Full diagram tool table + decision tree + selection factors
• `references/rendering-pitfalls.md` — Mermaid/LaTeX/wiki-link/collapsibles/universal-features + structural-consistency patterns 5-8 + systematic fix approach
• `references/academic-vault.md` — Academic study vault scaffold + per-chapter trio + content patterns (navigation/objectives/applied-understanding) + comprehensive coverage + CLAUDE.md layering
• `references/qa-checklist.md` — 50+ item QA checklist for declaring chapters/sections complete (content/format/structure/quality) + CLI verification commands + project template
• `references/voice-capture-macro.md` — QuickAdd + ElevenLabs MCP voice-memo-to-daily-note macro (working implementation as of 2026-05-15)

Status

v0.2.0 (2026-05-23 restructured per canonical agent-skills spec: <500 lines + companion docs in references/ subdirectory). Patterns are the result of a research arc with multi-wave agent verification, end-to-end mobile sync test, and Smart Connections empirical multilingual evaluation. NOT yet validated by an external full PKM build. Bump to v1.0 only after that lands.

The previously-separate obsidian-study-vault-builder skill (battle-tested across 37-file/828KB academic study vaults) was deprecated 2026-05-15 per PR #6 + post-compact re-validation. Its durable patterns are folded into this skill (references/academic-vault.md + references/qa-checklist.md + references/rendering-pitfalls.md § structural-consistency).