obsidian-organizer

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---
name: obsidian-organizer
description: >-
  File new notes into the right folder and audit/reorganize folder structure in
  the user's Obsidian vault, using the `obsidian` CLI and a single source-of-truth
  map note (`00_Index/Folder_Map.md`) that lives inside the vault. Use this
  whenever a note needs to be placed, filed, sorted, or moved into the vault;
  whenever the user asks where a note "belongs" or "should go"; and whenever they
  want to clean up, reorganize, deduplicate, audit, or restructure vault folders
  (e.g. orphaned notes, dead-end notes, near-duplicate titles, overlapping
  folders). Trigger even when the user just says "add this to my vault", "put
  this somewhere sensible", or "tidy up the cellchat notes" without naming a
  folder. Requires the Obsidian desktop app to be running.
---

# Obsidian Organizer

Keep a large Obsidian vault tidy over time by (1) filing new notes into the
best-fit folder and (2) auditing/reorganizing existing structure. Both modes lean
on one shared idea: a plain-markdown map of "what goes where" that lives **inside
the vault** so it never drifts out of sync with reality.

This skill drives the `obsidian` CLI (from the separate `obsidian-cli` skill),
which talks to the **live, running Obsidian desktop app**. The app must be open.
If a command fails with a connection/vault error, tell the user to open Obsidian
rather than guessing.

## Why the map lives in the vault (read this first)

Deciding a folder for every new note by re-listing ~650 folders is expensive and
guesses drift. Copying the folder taxonomy into Claude's private memory creates a
worse problem: a stale copy that silently disagrees with the real vault.

The fix is one file, `00_Index/Folder_Map.md`, checked into the vault itself. It
is the single source of truth for filing decisions. Read it with one cheap call
before you file or reorganize — do **not** re-run a full `obsidian folders`
traversal unless the map is missing or the user asks you to rebuild it.

```bash
obsidian read path="00_Index/Folder_Map.md"
```

It is deliberately plain markdown (headers + bullets, no required frontmatter) so
both you and the human can append to it by hand as new categories emerge. When you
create a new folder/category, add a line to this file so the next filing decision
remembers it.

If the map does not exist (deleted, or a fresh vault), rebuild it **from the live
vault**, not from a copy stashed in this skill — a bundled copy would drift from
reality, which is the whole failure this file exists to prevent. List the real
structure with `obsidian vault="MyVault" folders` (and `folders folder=...`
for depth), draft a plain-markdown map grouped by top-level PARA folder with a
short "what goes here" note per folder plus a filing rule-of-thumb, confirm the
groupings with the user, then create it:
`obsidian vault="MyVault" create path="00_Index/Folder_Map.md" content="..."`.

## Vault targeting

`MyVault` above is a placeholder — substitute the user's actual vault name
everywhere. If the user has more than one vault, target the intended one
explicitly on every command so a stray "most recently focused vault" default
cannot misfile a note:

```bash
obsidian vault="MyVault" read path="00_Index/Folder_Map.md"
```

`vault=` must be the **first** parameter. This is the only vault-specific value
in the skill — everything else comes from the vault's own `Folder_Map.md`.

## The one hard safety rule: never touch vault files with raw shell

When you relocate or rename a file, **always** use the CLI's own `move` / `rename`
commands. These go through Obsidian's API, so Obsidian's built-in "automatically
update internal links" behavior rewrites every wikilink and backlink across the
vault to follow the moved file. A raw `mv`, `rm`, `rmdir`, or `find -delete` on a
path inside the vault skips that repair and silently leaves broken links pointing
at the old location.

So, for anything under the vault directory:

- Move/rename → `obsidian move ...` or