Obsidian Second Brain — Setup & Audit

Overview

Complete setup guide for an Obsidian vault as a Second Brain with PARA methodology, Claude Code integration (MCP + hooks + skills), automated Git backup, and developer-focused workflows. Works from zero or audits/completes an existing setup.

When to Use

• Setting up a new Obsidian vault from scratch
• Auditing an existing vault for missing config/plugins/structure
• Adding Claude Code integration to an Obsidian vault
• Setting up automated backup with Git
• Configuring developer-focused PKM workflows (TILs, project context, investment tracking, hobby tracking)

Quick Reference

Implementation

Phase 1: Vault Structure (PARA)

Create the folder tree:

VaultRoot/
├── 00 - Inbox/                    # Quick capture, unprocessed notes
├── 00 - Dashboard.md              # Homepage with Dataview queries
├── 01 - Projetos/                 # Active projects with _contexto.md
│   └── ProjectName/
│       └── _contexto.md           # Project context file ("Gema")
├── 02 - Areas/                    # Permanent life domains
│   ├── Dev/TILs/                  # Today I Learned notes
│   ├── Investimentos/
│   │   ├── Ativos/                # Individual stock/asset notes
│   │   ├── Dividendos/            # Monthly dividend tracking
│   │   └── Analises/              # Investment analyses
│   ├── Hobbies/
│   │   ├── Anime/
│   │   ├── Manga/
│   │   ├── Games/
│   │   └── Board Games/
│   └── Pessoas/                   # Personal CRM
├── 03 - Recursos/                 # Reference material, links, clippings
├── 04 - Arquivo/                  # Completed/paused projects
├── 05 - Templates/                # Reusable note templates
├── 06 - Diario/                   # Daily notes (NEVER write here via Claude)
│   └── Semanas/                   # Weekly review notes
├── 07 - Claude/                   # Claude-generated analyses (write here)
└── CLAUDE.md                      # Root context for Claude Code

Phase 2: CLAUDE.md (Root Context)

Create CLAUDE.md at vault root with:

1. Identity: Owner name, role, objective, language
2. Vault structure: Folder tree with descriptions
3. Operation rules:
   • READ: Full vault access
   • WRITE ALLOWED: Only 07 - Claude/ and 00 - Inbox/
   • WRITE FORBIDDEN: Never overwrite 06 - Diario/ or personal notes
   • EDIT existing: Only with explicit permission
4. Project mapping: Table of project name → code repo path → stack
5. Tag system: Hierarchical + flat tags with examples
6. Skills reference: Table of available slash commands

Phase 3: Templates (7 templates)

All templates use {{date}} (YYYY-MM-DD) and {{title}} Templater variables.

Phase 4: Plugins (10 community plugins)

Install plugins to .obsidian/plugins/ and register in community-plugins.json.

Tier 1 (Essential):

Tier 2 (Power User):

Templater Folder Templates:

Periodic Notes Config:

Phase 5: Dashboard

Create 00 - Dashboard.md with Dataview queries for:

1. Projetos Ativos — TABLE from 01 - Projetos where _contexto exists
2. Tarefas Pendentes — Tasks query not done, sorted by due, limit 10
3. Inbox Pendente — LIST from 00 - Inbox, sorted by creation
4. Ultimas Notas — TABLE last 10 modified notes
5. Investimentos — TABLE from 02 - Areas/Investimentos/Ativos
6. TILs Recentes — TABLE from #til, last 5
7. Notas Orfas — LIST notes with 0 inlinks and 0 outlinks

Phase 6: Hotkeys

Configure .obsidian/hotkeys.json:

Phase 7: Git Backup

1. Init repo in vault root with .gitignore:

   .obsidian/workspace.json
   .obsidian/workspace
   .obsidian/plugins/obsidian-git/data.json
   .trash/
   .DS_Store
   Thumbs.db
   desktop.ini

2. Create private GitHub repo and push initial commit
3. Install obsidian-git plugin — auto-commits every 10 min when Obsidian is open
4. Cron job (15 min) for persistent backup even without Obsidian:

   #!/usr/bin/env bash
   VAULT="/path/to/vault"
   cd "$VAULT" || exit 0
   if git diff --quiet && git diff --cached --quiet && [ -z "$(git ls-files --others --exclude-standard)" ]; then
       exit 0
   fi
   git add --all
   git commit -m "vault: sync $(date +'%Y-%m-%d %H:%M')"
   git push origin main 2>/dev/null
   exit 0

   Register: */15 * * * * /path/to/vault-cron-sync.sh >> /tmp/vault-sync.log 2>&1
5. Ensure cron starts on boot (WSL: systemd=true in /etc/wsl.conf)

Phase 8: Claude Code Integration

MCP Server:

claude mcp add obsidian --scope user -- npx @mauricio.wolff/mcp-obsidian@latest "/path/to/vault"

• Filesystem-only (works without Obsidian GUI running)
• Path traversal protection, TOCTOU fixes

PostToolUse Hook (vault-autocommit.sh):

• Triggers on Write/Edit tools
• Auto-commits if file is inside the vault
• Runs async (non-blocking)
• Register in ~/.claude/settings.json under hooks.PostToolUse

Skills (install to ~/.claude/skills/):

Community Skills:

npx skills add kepano/obsidian-skills -g -a claude-code -y

Installs: obsidian-markdown, obsidian-bases, obsidian-cli, json-canvas, defuddle

Phase 9: Audit (Existing Vault)

When auditing an existing vault, check each layer:

1. PARA folders exist?           → Create missing ones
2. CLAUDE.md exists and current? → Create or update
3. Templates complete?           → Create missing, verify frontmatter
4. Plugins installed + configured? → Install missing, verify data.json
5. Dashboard exists?             → Create with Dataview queries
6. Hotkeys configured?           → Set up hotkeys.json
7. Git backup active?            → Init repo, .gitignore, cron, push
8. MCP server configured?       → Add via claude mcp add
9. Skills installed?             → Install community + custom skills
10. Hooks registered?            → Add PostToolUse auto-commit hook

Tag System

Hierarchical (group by domain)

#projeto/name          # Active project
#area/dev              # Development knowledge
#area/investimentos    # Investments
#area/investimentos/dividendos
#area/investimentos/acoes
#hobby/anime
#hobby/manga
#hobby/gaming
#hobby/boardgames

Flat (quick filter)

#til        #decisao      #ideia       #analise
#reflexao   #conexao      #ativo       #pausado
#concluido  #bug          #referencia  #pessoa

Common Mistakes