Markdown vault quality scanner for Obsidian, academics, and documentation teams
Markdown vault quality scanner for Obsidian, academics, and documentation teams. Exposed over MCP by the marginalia mcp server, that capability becomes something an assistant can invoke while it works, not something you go and do afterwards.
Zero dependencies. Pure Python. Works on any Markdown vault.
Everything the assistant can do here goes through one of these:
scan_status — Vault quality snapshot: files, tags, links, orphans, clusters, hubsquery_tags — Find files by exact tag or browse by namespace (e.g. domain/)get_related — Outgoing links + backlinks + tag affinity for a filelist_orphans — Orphan files with suggested parent links (sibling pattern)Prerequisites — If you don't have Python, install it from python.org/downloads — check "Add Python to PATH" duringUsage — The Usage tool exposed by this serverInstallation goes through your MCP client rather than a global install: point it at marginalia on PyPI and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.
You will need 5 environment variables: MARGINALIA_API_KEY, MARGINALIA_API_URL, OPENROUTER_API_KEY, DEEPSEEK_API_KEY, OPENAI_API_KEY. The server will not start without them, which is usually why the tools fail to appear on a first run. Keep credentials in your client's env block or a secrets manager rather than in a file you might commit.
You need Python 3.9 or newer. Check if you have it: If you don't have Python, install it from python.org/downloads — check "Add Python to PATH" during installation.
Among the team communication options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. Marginalia's toolset — scan_status, query_tags, get_related and 3 more — is a fair guide to whether it matches your workflow.
This entry was verified against Marginalia's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| Tool | What it does |
|---|---|
| scan_status | Vault quality snapshot: files, tags, links, orphans, clusters, hubs |
| query_tags | Find files by exact tag or browse by namespace (e.g. domain/) |
| get_related | Outgoing links + backlinks + tag affinity for a file |
| list_orphans | Orphan files with suggested parent links (sibling pattern) |
| Prerequisites | If you don't have Python, install it from [python.org/downloads](https://www.python.org/downloads/) — check **"Add Python to PATH"** during installation. |
| Usage | The Usage tool exposed by this server. |
{
"mcpServers": {
"marginalia-mcp": {
"command": "cmd",
"args": ["/c", "marginalia-mcp", "--vault", "C:\\path\\to\\vault"]
}
}
}Configuration as documented by the project. Restart the client after saving.
You need Python 3.9 or newer. Check if you have it: If you don't have Python, install it from python.org/downloads — check "Add Python to PATH" during installation.
| Variable | Description | Required |
|---|---|---|
| MARGINALIA_API_KEY | Credential the server authenticates with. | Yes |
| MARGINALIA_API_URL | Endpoint or connection string the server talks to. | Yes |
| OPENROUTER_API_KEY | Credential the server authenticates with. | Yes |
| DEEPSEEK_API_KEY | Credential the server authenticates with. | Yes |
| OPENAI_API_KEY | Credential the server authenticates with. | Yes |
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