Obsidian Agentic Vault

A reproducible Obsidian vault template for working with AI coding/writing agents (Claude Code, Codex, Perplexity, Antigravity, ...) directly against your notes.

The core idea, borrowed from Nick Milo's PKM approach: every agent points at a single 90 Meta/Skills/ folder in the vault. Each skill is a self-contained note (or folder) describing a repeatable task — how to write a daily note, how to triage the inbox, how to format a literature note, etc. Agents read this folder to learn how you want work done, so you only maintain the instructions once and every tool benefits.

The folder layout follows Tiago Forte's PARA method (Projects, Areas, Resources, Archive) from Building a Second Brain, numbered by actionability. Folders are kept flat — 20 Projects/ is the only place that gets per-item subfolders, since a project is self-contained (notes, drafts, and files for one project live together). MOCs (Maps of Content) are plain notes tagged moc, not a separate folder.

Structure

.
├── 00 Inbox/            # Unprocessed capture - triage out of here daily/weekly.
├── 10 Journals/         # Daily/weekly logs.
├── 20 Projects/         # Active, has a deadline/outcome. Self-contained per project
│   └── <project>/       # subfolder - the only folder that nests further.
│       ├── <project>.md # link target for the rest of the vault.
│       ├── INDEX.md     # project structure - see manage-project skill.
│       ├── CONTEXT.md   # short current-state snapshot, overwritten each time.
│       └── LOG.md       # thorough append-only history.
├── 30 Areas/            # Ongoing responsibilities, no end date.
├── 40 Resources/        # Topic reference material, no immediate action.
│   └── Literature/      # Literature source notes from ZotFlow.
├── 50 Notes/            # Permanent, atomic notes - includes MOCs (tag: moc).
├── 60 Bases/            # Obsidian Bases / databases.
├── 90 Meta/
│   ├── Skills/          # One skill per subfolder. The shared "brain" all agents read.
│   └── Templates/       # Obsidian note templates (Templater/core Templates plugin).
│       └── Project/     # Templates for <project>.md, INDEX.md, CONTEXT.md, LOG.md.
├── 99 Archive/          # Inactive items, mirrored by category.
│   ├── Projects/
│   ├── Areas/
│   ├── Resources/
│   └── Literature/
├── .obsidian/           # Obsidian app config (community plugins, hotkeys, etc).
├── CLAUDE.md            # Entry point for Claude Code.
├── AGENTS.md            # Entry point for Codex (and other agents that read AGENTS.md).
└── .perplexity/         # Perplexity Spaces instructions.

Community plugins used

Bundled under .obsidian/plugins/ (enabled via community-plugins.json):

• Tasks (obsidian-tasks-plugin) - task management via #task in note bodies.
• ZotFlow (zotflow) - Zotero integration for literature notes.
• Hidden Folders Access (hidden-folders-access) - indexes hidden root-level folders (e.g. .claude) so they appear in the file tree, metadata cache, and Bases.

Not bundled (install via Obsidian's Community Plugins browser if you use them):

• Copilot - AI chat/assistant against vault content.
• Templater - powers the templates under 90 Meta/Templates/.

Setting up your own vault

1. Use this repo as a template (or copy its contents into your existing vault).
2. Open the folder in Obsidian and enable the community plugins you use (see Community plugins used above - the bundled ones just need enabling, the rest install as needed).
3. Add/edit skills under 90 Meta/Skills/ - see 90 Meta/Skills/example-skill/SKILL.md for the format.
4. Point each agent at the vault root:
   • Claude Code: reads CLAUDE.md, which links to 90 Meta/Skills/.
   • Codex: reads AGENTS.md, which links to 90 Meta/Skills/.
   • Perplexity: paste/sync .perplexity/instructions.md into your Space instructions.
   • Antigravity: point its project/context config at 90 Meta/Skills/ the same way (see AGENTS.md - Antigravity reads the same conventions).
5. Commit your vault to git (recommended) so every agent's edits are versioned and reviewable.

Adding a new skill

90 Meta/Skills/<skill-name>/SKILL.md

Each SKILL.md should state: when to use the skill, the steps to follow, and any templates/files it depends on (templates live under 90 Meta/Templates/). Keep skills small and single-purpose - compose multiple skills for bigger workflows rather than writing one giant skill.

Bundled skills

• example-skill/ - triaging a new inbox note into the right PARA folder.
• create-moc/ - creating/updating Maps of Content once a topic has accumulated enough notes.
• manage-project/ - the project-note/INDEX.md/CONTEXT.md/LOG.md convention for 20 Projects/.
• frontmatter/ - canonical YAML frontmatter fields per note type, so Bases/Dataview queries stay reliable.
• vault-lint/ - periodic health-check for broken links, orphan notes, missing frontmatter, and stale project context.
• weave-trails.md - periodic pass that proposes links between related but unconnected permanent notes and flags emerging hubs for promotion to a MOC (Memex/Zettelkasten/Evergreen-Notes-style associative linking).
• update-skills/ - syncing 90 Meta/Skills/ against the public template repo this vault was created from.
• update-vault-structure/ - reconciling the vault's shared framework (folders, templates) against the public template repo.
• obsidian-markdown/ - Obsidian Flavored Markdown syntax (wikilinks, embeds, callouts, properties).
• obsidian-bases/ - creating/editing .base files (views, filters, formulas, summaries).
• obsidian-cli/ - reading/creating/searching notes and managing plugins/themes from the command line via the Obsidian CLI.
• json-canvas/ - creating/editing .canvas files (mind maps, flowcharts, visual boards).
• defuddle/ - extracting clean markdown from web pages instead of fetching raw HTML.

The last five are vendored from kepano/obsidian-skills (MIT, see 90 Meta/Skills/THIRD_PARTY_NOTICES.md).