Obsidian Commander

Full-featured Obsidian vault management from any code editor or CLI. Supports VS Code (GitHub Copilot), Claude Code, Cursor, Copilot CLI, Claude CLI, and any agent-compatible IDE.

When to Use

• Create, read, update, delete notes in a vault
• Search vault content (text, semantic, tags, properties)
• Manage frontmatter/properties (add, edit, remove, bulk update)
• Map and audit links (backlinks, orphans, unresolved, dead-ends)
• Clean up vault (remove orphans, fix broken links, deduplicate)
• Organize vault structure (move notes, create folders, apply templates)
• Build and query a semantic search index
• Ingest external content into the vault
• Generate vault health reports
• Manage daily notes, tasks, bookmarks, templates
• Control Obsidian app via CLI (requires Obsidian 1.12.7+)

Quick Decision: CLI vs File-Based

Vault Detection

Before any operation, locate the vault:

1. Check if current working directory contains .obsidian/ folder
2. If not, ask user for vault path
3. Validate: vault must contain .obsidian/ directory

vault_path = find_ancestor_with(".obsidian") or ask_user("Vault path?")

Core Procedures

1. Create a Note

# Via Obsidian CLI (if running)
obsidian create name="My Note" content="# My Note\n\nContent here"

# Via file system
# Create file at <vault>/path/Note.md with frontmatter

Template for new note:

---
created: {{date}}
tags: []
aliases: []
---

# {{title}}

{{content}}

Use [createnote.py](./scripts/createnote.py) for advanced creation with templates and auto-linking.

2. Search the Vault

Text search (Obsidian CLI):

obsidian search query="meeting notes"
obsidian search:context query="TODO" path="Projects/"

Semantic search (AI-powered, works offline):

python scripts/semantic_search.py --vault /path/to/vault --action build   # Index
python scripts/semantic_search.py --vault /path/to/vault --action ask --query "concept"

Property search (find notes by metadata):

python scripts/search_properties.py --vault /path/to/vault --property status --value "draft"

Search operators reference (for Obsidian CLI):

3. Manage Properties / Frontmatter

Read properties:

obsidian properties active                    # Current file
obsidian property:read name=tags file=MyNote  # Specific property

Set properties:

obsidian property:set name=status value=published file=MyNote
obsidian property:set name=tags value="[project,active]" type=list

Bulk update (use script for batch operations):

python scripts/bulk_properties.py --vault . --filter "tag:#draft" --set "status=review"
python scripts/bulk_properties.py --vault . --folder "Archive/" --set "archived=true" --type checkbox

Property types: text, list, number, checkbox, date, datetime

YAML frontmatter format:

---
title: My Note
tags:
  - project
  - active
created: 2024-01-15
status: draft
aliases:
  - "my-note"
cssclasses:
  - wide-page
---

4. Map and Audit Links

List links:

obsidian links file=MyNote          # Outgoing links
obsidian backlinks file=MyNote      # Incoming links
obsidian unresolved                 # Broken links in vault
obsidian orphans                    # Notes with no incoming links
obsidian deadends                   # Notes with no outgoing links

Full link audit (comprehensive report):

python scripts/link_audit.py --vault /path/to/vault

Output:

=== Vault Link Health Report ===
Total notes: 342
Total links: 1,205
Resolved: 1,180 (97.9%)
Unresolved: 25
Orphan notes: 18
Dead-end notes: 45
Bidirectional links: 380

Link formats in Obsidian:

• Wikilinks: [[Note Name]], [[Note Name|Display Text]], [[Note#Heading]], [[Note#^block-id]]
• Markdown: [Display](Note.md), [Display](Note.md#Heading)
• Embeds: ![[Note]], ![[image.png]]

5. Clean Up Vault

python scripts/vault_cleanup.py --vault /path/to/vault --action report  # Dry run
python scripts/vault_cleanup.py --vault /path/to/vault --action fix     # Apply fixes

Cleanup operations:

• Remove empty notes (no content beyond frontmatter)
• Fix broken internal links
• Remove duplicate notes
• Standardize frontmatter (ensure required fields)
• Clean orphaned attachments (images/files not linked anywhere)
• Normalize tag casing
• Remove stale TODO items

6. Organize Vault Structure

Move and rename:

obsidian move file=OldNote to="Archive/2024/"
obsidian rename file=OldName name="New Name"

Batch organize:

python scripts/organize_vault.py --vault . --strategy by-tag      # Group by primary tag
python scripts/organize_vault.py --vault . --strategy by-date     # Group by creation date
python scripts/organize_vault.py --vault . --strategy by-moc      # Group around Maps of Content

Create folder structure from template:

python scripts/scaffold_vault.py --vault . --template zettelkasten
python scripts/scaffold_vault.py --vault . --template para
python scripts/scaffold_vault.py --vault . --template gtd

Available templates: zettelkasten, para (Projects/Areas/Resources/Archive), gtd, journal, research, custom

7. Ingest External Content

python scripts/ingest.py --vault . --source /path/to/files --format markdown
python scripts/ingest.py --vault . --source /path/to/files --format html --convert
python scripts/ingest.py --vault . --source clipboard --as daily-append
python scripts/ingest.py --vault . --url "https://example.com/article" --as note

Supported source formats: Markdown, HTML, plain text, PDF (text extraction), CSV, JSON Ingestion modes:

• note: Create a new note per file
• append: Append to an existing note
• daily-append: Append to today's daily note
• split: Split large documents into linked notes

8. Build Semantic Search Index

Uses sentence-transformers and FAISS for AI-powered semantic search:

# Build/rebuild index
python scripts/semantic_search.py --vault /path/to/vault --action build

# Query
python scripts/semantic_search.py --vault /path/to/vault --action ask --query "machine learning concepts" --top 10

# Incremental update (only new/modified notes)
python scripts/semantic_search.py --vault /path/to/vault --action update

Requirements: pip install -r requirements.txt (sentence-transformers, faiss-cpu, numpy, pyyaml, tqdm)

9. Daily Notes & Tasks

# Daily notes
obsidian daily                                          # Open today's daily note
obsidian daily:append content="- [ ] Buy groceries"     # Add task
obsidian daily:read                                     # Read content

# Tasks
obsidian tasks todo                                     # List incomplete tasks
obsidian tasks daily                                    # Tasks from daily note
obsidian task ref="Recipe.md:8" toggle                  # Toggle task

10. Templates

obsidian templates                                      # List templates
obsidian template:read name=Meeting resolve             # Preview with variables
obsidian create name="Standup 2024-01-15" template=Meeting

11. Vault Health Check

python scripts/vault_health.py --vault /path/to/vault

Report includes:

• Total notes, attachments, tags, properties
• Link health (resolved %, orphans, dead-ends, unresolved)
• Frontmatter consistency (missing required fields)
• Tag distribution and potential duplicates
• Large files and potential splits
• Recently modified vs stale notes
• Naming convention violations

12. Manage Plugins & Themes (via CLI)

obsidian plugins                                        # List installed
obsidian plugin:install id=dataview enable               # Install + enable
obsidian plugin:reload id=my-plugin                      # Reload (dev)
obsidian themes                                          # List themes
obsidian theme:set name="Minimal"                        # Set theme

Obsidian Data Model Reference

Vault structure:

my-vault/
├── .obsidian/                 # Config folder (hidden)
│   ├── app.json               # App settings
│   ├── appearance.json        # Theme settings
│   ├── community-plugins.json # Installed plugins list
│   ├── core-plugins.json      # Core plugin toggles
│   ├── hotkeys.json           # Custom hotkeys
│   ├── plugins/               # Plugin data & settings
│   ├── themes/                # Installed themes
│   ├── snippets/              # CSS snippets
│   └── workspace.json         # Layout (exclude from git)
├── Notes/                     # Your notes (any structure)
├── Templates/                 # Template files
├── Attachments/               # Images, PDFs, etc.
└── Daily Notes/               # Daily notes folder

Frontmatter (YAML between --- markers):

• Default properties: tags (list), aliases (list), cssclasses (list)
• Custom properties: any key-value pairs
• Types: text, list, number, checkbox, date, datetime

Link syntax:

Tags: #tag, #nested/tag, in frontmatter as tags: [a, b]

Workflow Examples

"I want to capture a quick idea"

obsidian create name="Idea - Quantum Computing" content="# Quantum Computing\n\n- Potential for ML acceleration\n- Read more about Shor's algorithm" open
obsidian property:set name=tags value="[idea,quantum,research]" type=list

"Show me everything related to Project X"

obsidian search query="Project X"
obsidian search:context query="tag:#project-x"
python scripts/semantic_search.py --vault . --action ask --query "Project X goals and deliverables"

"Clean up my vault"

python scripts/vault_health.py --vault .
python scripts/vault_cleanup.py --vault . --action report
python scripts/vault_cleanup.py --vault . --action fix

"Reorganize by PARA method"

python scripts/scaffold_vault.py --vault . --template para
python scripts/organize_vault.py --vault . --strategy by-tag --mapping "project:Projects,area:Areas,resource:Resources,archive:Archive"