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Agent skill

Obsidian Vault Setup

by Atmosphere in Atmosphere/atmosphere

A skill your agent uses when setting up the shared atmosphere-vault Obsidian vault on a new machine or for a new team member.

Apache-2.0Auto-check passedKnowledge Management

Install Obsidian Vault Setup

skills CLI
$ npx skills add Atmosphere/atmosphere --skill obsidian-vault-setup -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install Atmosphere/atmosphere obsidian-vault-setup --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/Atmosphere/atmosphere.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/obsidian-vault-setup .claude/skills/obsidian-vault-setup && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
obsidian-vault-setup
GitHub stars
3.8k
Token cost
~1.2k tokens
SKILL.md length
428 words
Files
1
Skills in repo
20
Repo updated
First seen
Licence
Apache-2.0

At a glance

A skill your agent uses when setting up the shared atmosphere-vault Obsidian vault on a new machine or for a new team member.

  • Works in 6 steps: Verify prerequisites → Clone atmosphere-vault → Install plugins → …
  • Setting up the shared atmosphere-vault Obsidian vault on a new machine
  • SKILL.md covers Role, When to Use, Defaults and Workflow, plus 2 more sections
  • Calls git, claude and npm; reaches obsidian.md

What it does

Obsidian Vault Setup is an agent skill from Atmosphere/atmosphere. Use when setting up the shared atmosphere-vault Obsidian vault on a new machine or for a new team member. Guides through cloning, installing plugins, symlinking claudedocs, and verifying the Obsidian CLI.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Knowledge Management. It works with Obsidian, npm and Git. The repository describes itself as: Portable AI agent runtime for the JVM. One @Agent class runs on Spring AI, LangChain4j, Anthropic, or 9 more behind one SPI. Token streaming, tool calls, human approvals, and… The licence is Apache-2.0.

When your agent uses it

  • Setting up the shared atmosphere-vault Obsidian vault on a new machine
  • For a new team member

Example prompts

  • “/obsidian-vault-setup”

Workflow steps

6 steps, taken from the step headings in SKILL.md.

  1. Verify prerequisites
  2. Clone atmosphere-vault
  3. Install plugins
  4. Create claude_docs symlink
  5. Open vault in Obsidian
  6. Verify sync flow

What it can do on your machine

Read from SKILL.md and the folder at commit 13671cf. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • git
    • claude
    • npm

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • obsidian.md

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Obsidian Vault Setup loads about 1.2k tokens when it runs. Until then it costs about 57 tokens; SKILL.md has 428 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~57
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from Atmosphere/atmosphere at commit 13671cf, republished under its Apache-2.0 licence (© Atmosphere). 428 words, ~1,221 tokens.

Download SKILL.mdSave it as .claude/skills/obsidian-vault-setup/SKILL.md (or your agent's skills folder).
name
obsidian-vault-setup
description
Use when setting up the shared atmosphere-vault Obsidian vault on a new machine or for a new team member. Guides through cloning, installing plugins, symlinking claude_docs, and verifying the Obsidian CLI.
user-invocable
true
metadata.version
1.1.0
metadata.domain
devops
metadata.triggers
obsidian, vault, setup, onboard, atmosphere-vault
metadata.role
specialist
metadata.scope
implementation
metadata.output-format
report

Obsidian Vault Setup

Role

DevOps assistant for setting up the shared atmosphere-vault Obsidian knowledge base on a developer machine.

When to Use

Invoke when a team member needs to:

  • Clone and open the atmosphere-vault for the first time
  • Connect their atmosphere checkout to the vault via symlink
  • Verify the Obsidian CLI and the vault's commit timer are configured correctly

Defaults

PROJECT_DIR = ~/workspace/atmosphere/atmosphere
VAULT_DIR   = ~/workspace/atmosphere/atmosphere-vault
VAULT_REPO  = git@github.com:Atmosphere/atmosphere-vault.git

Ask the user for PROJECT_DIR and VAULT_DIR if they differ from defaults. The vault is a sibling of the project directory: the routing block reaches it as ../atmosphere-vault, and the vault's scripts/sync-claude-memory.sh reaches the checkout as ../atmosphere.

Workflow

Step 1: Verify prerequisites

Check that the following are installed:

bash
# Obsidian desktop app (required)
ls /Applications/Obsidian.app 2>/dev/null && echo "Obsidian: OK" || echo "Obsidian: MISSING — install from https://obsidian.md"

# The app's own CLI (Settings → General → enable the command line interface)
command -v obsidian   # must print /Applications/Obsidian.app/Contents/MacOS/obsidian

If command -v obsidian prints an npm path, the unrelated obsidian-cli npm package is shadowing the real CLI — npm uninstall -g obsidian-cli.

Step 2: Clone atmosphere-vault
bash
# Only if not already present
if [ ! -d "$VAULT_DIR" ]; then
  git clone git@github.com:Atmosphere/atmosphere-vault.git "$VAULT_DIR"
fi

# Verify on main branch
cd "$VAULT_DIR" && git status
Step 3: Install plugins

Downloads obsidian-git and Templater and writes their pre-configured settings.

bash
cd "$VAULT_DIR"
./scripts/install-plugins.sh

This script:

  • Downloads main.js + manifest.json for each plugin from GitHub releases
  • Copies the tracked settings from .obsidian/plugin-configs/ into each plugin's data.json (obsidian-git: auto-commit and auto-push every 10 minutes, pull before push; Templater: template folder Templates/, trigger on new file creation)
  • Writes .obsidian/community-plugins.json to enable both plugins

Plugin binaries are excluded from git (.obsidian/plugins/ is in .gitignore). Re-running the script is safe — it overwrites existing files idempotently.

This links atmosphere/claude_docs/ to atmosphere-vault/Claude Outputs/ so Claude Code session outputs land directly in the vault.

bash
cd "$PROJECT_DIR"

# Safety check: do NOT overwrite a real directory
if [ -d claude_docs ] && [ ! -L claude_docs ]; then
  echo "ERROR: claude_docs/ exists as a real directory. Back it up before proceeding."
  exit 1
fi

ln -sf "$VAULT_DIR/Claude Outputs" claude_docs
ls -la claude_docs   # verify symlink resolves
Show full SKILL.md (194 more words)Show less
Step 5: Open vault in Obsidian

Instruct the user to:

  1. Open Obsidian
  2. Click Open folder as vault
  3. Navigate to $VAULT_DIR and click Open
  4. When prompted "Trust and enable plugins?", click Trust author and enable plugins

The vault's commit timer is obsidian-git's, configured by Step 3 to commit and push every 10 minutes. Run exactly one per machine: if the machine already runs another commit timer of its own for the vault (nothing in this repo or the vault ships one), set obsidian-git's auto-commit and auto-push intervals to 0 there.

Step 6: Verify sync flow

After obsidian-git is configured:

bash
# Create a test file in Claude Outputs
echo "# Test" > "$PROJECT_DIR/claude_docs/test.md"

# Verify it appears in the vault
ls "$VAULT_DIR/Claude Outputs/test.md"

# Clean up
rm "$PROJECT_DIR/claude_docs/test.md"

Constraints

  • NEVER overwrite an existing claude_docs/ directory that contains real files
  • ALWAYS verify atmosphere-vault is on main branch before linking
  • NEVER install the npm obsidian-cli package — it shadows the app's own obsidian CLI
  • If PROJECT_DIR or VAULT_DIR differ from defaults, ask for them before running any commands

Success Criteria

  • ls -la $PROJECT_DIR/claude_docs shows a symlink pointing to $VAULT_DIR/Claude Outputs
  • Obsidian opens the vault and shows all folders (Architecture, APIs, Methodology, Development)
  • command -v obsidian resolves to the app bundle
  • Exactly one commit timer commits into the vault on this machine (Step 5)

© Atmosphere, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .claude/skills/obsidian-vault-setup of Atmosphere/atmosphere.

Open the folder on GitHubat commit 13671cf

Compare with similar skills

Obsidian Vault Setup next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Obsidian Vault Setup compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Obsidian Vault Setup this skillAtmosphere/atmosphere3.8k—~1.2kAutomated safety check: PassApache-2.0
Release New Versiondanzilberdan/obsidian-mathlive159—~444Automated safety check: PassMIT
Obsidian Plugin Releasecrafter-station/skills112—~1.8kAutomated safety check: PassMIT
Logseq Plugin SDKlogseq/logseq45k—~2.3kAutomated safety check: PassAGPL-3.0
Docs Managementbkywksj/knowledge-base330—~2.5kAutomated safety check: PassCustom licence
LLM WikiCharlesHoskinson/sevenlayer116—~1.5kAutomated safety check: PassCustom licence

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Works with

Categories

Questions about Obsidian Vault Setup

What does Obsidian Vault Setup do?

A skill your agent uses when setting up the shared atmosphere-vault Obsidian vault on a new machine or for a new team member. Obsidian Vault Setup is an agent skill from Atmosphere/atmosphere. Use when setting up the shared atmosphere-vault Obsidian vault on a new machine or for a new team member.

When should I use Obsidian Vault Setup?

Obsidian Vault Setup fits situations like: setting up the shared atmosphere-vault Obsidian vault on a new machine; for a new team member.

How do I install Obsidian Vault Setup in Claude Code?

Run `npx skills add Atmosphere/atmosphere --skill obsidian-vault-setup -a claude-code`. Or copy the skill folder (.claude/skills/obsidian-vault-setup in Atmosphere/atmosphere) into .claude/skills/obsidian-vault-setup in your project. Claude Code loads it when a task matches its description.

How do I install Obsidian Vault Setup in Codex?

Run `npx skills add Atmosphere/atmosphere --skill obsidian-vault-setup -a codex`. Or copy the skill folder (.claude/skills/obsidian-vault-setup in Atmosphere/atmosphere) into .agents/skills/obsidian-vault-setup in your project. Codex loads it when a task matches its description.

Can I use Obsidian Vault Setup in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Atmosphere/atmosphere --skill obsidian-vault-setup -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/obsidian-vault-setup, .gemini/skills/obsidian-vault-setup, .github/skills/obsidian-vault-setup and .opencode/skills/obsidian-vault-setup in your project.

What does Obsidian Vault Setup need to run?

Going by SKILL.md and its folder, Obsidian Vault Setup needs the command-line tools its instructions call (git, claude and npm).

Does Obsidian Vault Setup access the network?

SKILL.md names 1 domain. In commands or code: obsidian.md; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Obsidian Vault Setup safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Obsidian Vault Setup use?

Obsidian Vault Setup is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Obsidian Vault Setup use?

About 1.2k tokens (SKILL.md is roughly 4.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Obsidian Vault Setup?

Skills that share tags, products or a category with Obsidian Vault Setup: Release New Version (danzilberdan/obsidian-mathlive, 159 stars), Obsidian Plugin Release (crafter-station/skills, 112 stars), Logseq Plugin SDK (logseq/logseq, 45k stars) and Docs Management (bkywksj/knowledge-base, 330 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Obsidian Vault Setup?

Atmosphere (a GitHub organization) maintains it in Atmosphere/atmosphere, which has 3,818 GitHub stars. The repository holds 20 skills in this directory. The repository was last updated on October 6, 2026.

Source: Atmosphere/atmosphere on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.