Obsidian Init (Vault Onboarding)

Status: Active Author: Richard Fremmerlid Domain: Obsidian Integration

Purpose

This skill is the entry point for any project adopting Obsidian. It handles:

Verifying (and guiding installation of) prerequisites
Initializing the vault configuration
Setting up exclusion filters
Validating the vault is ready for agent operations

Phase 1: Prerequisites Installation

1.1 Obsidian Desktop Application (Required)

The Obsidian desktop app must be installed on the host machine. It is the visual interface for browsing, editing, and viewing the Graph and Canvas.

macOS (Homebrew):

brew install --cask obsidian

Manual Download:

https://obsidian.md/download

Verify:

ls /Applications/Obsidian.app

1.2 Obsidian CLI v1.12+ (Recommended)

The official CLI communicates with a running Obsidian instance via IPC singleton lock. It enables programmatic vault operations (read, search, backlinks, properties).

npm (global install):

npm install -g obsidian-cli

Verify:

obsidian --version

Note: The CLI requires an active Obsidian Desktop instance to communicate with. It operates in "silent" mode by default. For headless/CI environments where Obsidian is not running, our vault_ops.py (from obsidian-vault-crud) handles direct filesystem operations without requiring the CLI.

1.3 ruamel.yaml (Required for CRUD Operations)

Lossless YAML frontmatter handling requires ruamel.yaml:

pip install ruamel.yaml

1.4 Optional Community Plugins

For advanced vault features, install these from within the Obsidian app:

Plugin	Purpose	Required For
Dataview	Database-style queries over frontmatter	Structured metadata queries
Canvas (built-in)	Visual boards with JSON Canvas spec	`obsidian-canvas-architect` skill
Bases	Table/grid/card views from YAML	`obsidian-bases-manager` skill

Phase 2: Vault Initialization

Interactive Init

python ./scripts/init_vault.py --vault-root <path>

With Custom Exclusions

python ./scripts/init_vault.py \
  --vault-root <path> \
  --exclude "custom_dir/" "*.tmp"

Validate Only (No Changes)

python ./scripts/init_vault.py --vault-root <path> --validate-only

What It Does

Validates the target directory exists and contains .md files
Creates the .obsidian/ configuration directory (if not present)
Writes app.json with sensible exclusion filters for developer repos
Updates .gitignore to exclude .obsidian/ (user-specific config)
Reports next steps for opening the vault in the Obsidian app

Phase 3: Exclusion Configuration

Default Exclusions

Pattern	Reason
`node_modules/`	NPM dependencies
`.worktrees/`	Git worktree isolation
`.vector_data/`	ChromaDB binary data
`.git/`	Git internals
`venv/`	Python virtual environments
`__pycache__/`	Python bytecode cache
`*.json`	Data/config files (not knowledge)
`*.jsonl`	Export payloads
`learning_package_snapshot.md`	Machine-generated bundle
`bootstrap_packet.md`	Machine-generated bundle
`learning_debrief.md`	Machine-generated bundle
`*_packet.md`	Audit/review bundles
`*_digest.md`	Context digests
`dataset_package/`	Export artifacts

Why Exclude Machine-Generated Files?

These are giant concatenated snapshots produced by bundler/distiller scripts. Indexing them in Obsidian would pollute the graph with thousands of false backlinks pointing into machine-generated text, not human-authored knowledge.

Phase 4: Post-Init Steps

Open Obsidian → Click "Open Folder as Vault" → Select vault root
Verify indexing → Check that 01_PROTOCOLS/, ADRs/, etc. appear in sidebar
Test wikilinks → Click any [[link]] to confirm navigation works
Set VAULT_PATH → export VAULT_PATH=/path/to/vault

Portability Note

This skill is project-agnostic. It works on any Git repository with markdown files. The exclusion filters are sensible defaults for developer projects. When reusing this plugin in other projects, simply run the init script with the new project's root path.

Quick Reference: Full Install Sequence

# 1. Install prerequisites
brew install --cask obsidian        # Desktop app
npm install -g obsidian-cli         # CLI tools
pip install ruamel.yaml             # Lossless YAML

# 2. Initialize vault
python ./scripts/init_vault.py \
  --vault-root /path/to/your/project

# 3. Set environment variable
export VAULT_PATH=/path/to/your/project

# 4. Open in Obsidian app
open /Applications/Obsidian.app

obsidian-init