Obsidian init

Dependencies

This skill requires Python 3.8+ and standard library only. No external packages needed.

To install this skill's dependencies:

pip-compile ./requirements.in
pip install -r ./requirements.txt

See ./requirements.txt for the dependency lockfile (currently empty — standard library only).

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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:

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

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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

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Phase 2: Vault Initialization

Interactive Init

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

With Custom Exclusions

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

Validate Only (No Changes)

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

What It Does

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

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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.

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Phase 4: Post-Init Steps

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

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Phase 5: Wiki Engine Initialization (Guided Discovery Sub-Agent)

After the vault is initialized, you can optionally initialize the LLM Wiki Engine layer. This creates a wiki_sources.json manifest — the multi-source registry that tells the wiki engine which raw content folders to index.

This is the wiki equivalent of rlm_profiles.json in the RLM system. Each named entry in wiki_sources.json is a raw content directory that will be parsed into Karpathy-style wiki nodes. No files are moved.

5.1 Run the Guided Discovery Sub-Agent

The sub-agent interviews you interactively to register your raw content directories:

/wiki-init

Or directly:

python ./scripts/raw_manifest.py --init --wiki-root /path/to/wiki-root

5.2 What the Sub-Agent Asks

For each source folder you want to index, it asks:

Question	Example Answer
Wiki root path?	/path/to/vault/wiki-root
Source folder path?	/path/to/vault/notes
Label for this source?	daily-notes
File extensions?	.md (default)
Subdirectories to exclude?	_archive, *.tmp
Add another source?	yes/no

5.3 Output: rlm_wiki_raw_sources_manifest.json

Uses the same flat schema as rlm-factory and vector-db for consistency:

{
  "description": "Source raw content for Obsidian Wiki",
  "include": [
    "plugins/",
    "plugin-research/"
  ],
  "exclude": [
    ".git/",
    "node_modules/",
    ".venv/",
    "__pycache__/"
  ],
  "recursive": true
}

Saved to: .agent/learning/rlm_wiki_raw_sources_manifest.json

5.4 Next Steps After Discovery

/wiki-ingest    <- parse all registered sources, build wiki nodes
/wiki-distill   <- generate RLM summaries (cheapest available LLM CLI)
/wiki-query     <- start querying the wiki

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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 ./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