MCP server for Obsidian vault structural health checks. Find broken wikilinks, orphaned notes, and missing frontmatter — then auto-repair them.
Your Obsidian vault is slowly rotting. You just can't see it yet.
A note gets renamed and its wikilinks silently break. A file gets created without frontmatter and becomes invisible to Dataview. An orphan is born when its only incoming link gets deleted. A year in, you have 1,500 notes and no idea which ones are still wired correctly — because the rot is distributed across thousands of tiny local breakages that never raise a flag.
Vault Health is the audit. Point it at any Obsidian vault and get a full structural report in seconds: every broken [[wikilink]] with source and target, every
orphan note with zero inbound links, every file missing required frontmatter. Then — for the safe categories only — one call auto-repairs.
Six tools, covering the full diagnose → fix loop:
- check_vault_health — full scan; categorized list of every issue found
- find_broken_links — just the broken wikilinks, with source and target
- find_orphans — leaf notes with no inbound link from any hub or branch
- vault_statistics — size, link count, orphan %, frontmatter coverage
- repair_vault — auto-fix the safe categories; additive-only, never deletes or overwrites
- configure_vault — point at a different vault any time
Auto-repair is safe by design. Broken [[links]] get replaced with plain text (the link text is preserved, so nothing is lost). Missing frontmatter gets a
minimal default block added. Nothing is ever deleted. Nothing that already exists gets overwritten. You can run it on a production vault without a backup — the
worst case is that some broken links become plain text, which they effectively already were.
Why it matters. A vault that can't be trusted isn't a knowledge base — it's a junk drawer. When your AI queries Obsidian and hits stale paths or invisible
notes, answers degrade silently. Vault Health turns the invisible decay into a concrete, actionable list. Run it weekly, after a refactor, or before handing the
vault to a collaborator.
Works with any vault — no plugin required, no Obsidian running, no cloud. Pure filesystem analysis: markdown and YAML in, diagnosis and safe repair out.