Reorganize

Reorganize Vault

This skill handles two scenarios:

• Legacy migration (old 5-folder → new 8-folder structure): adds 02-areas/, 04-resources/, 05-agent/, renumbers archive/logs. Run this if your vault was set up before the 8-folder layout.
• Subfolder migration (original purpose, unchanged): moves flat notes into kebab-case subfolders within their existing folders.

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Before You Begin

Check vault version: Read onebrain.yml. If the folders.areas key is absent, this vault uses the old structure and needs full migration : run the Full Migration section first. If folders.areas is present, skip to the Subfolder Migration section.

Important: Obsidian wikilinks ([[Note Name]]) resolve by filename regardless of path : moving files does NOT break any existing links in your vault.

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Full Migration (5-folder → 8-folder)

Only run if onebrain.yml is missing folders.areas.

1. Create new folders: 02-areas/, 04-resources/, 05-agent/memory/
2. Rename 03-archive/ → 06-archive/: move all contents preserving YYYY/MM/ structure
3. Rename 04-logs/ → 07-logs/: move all contents preserving YYYY/MM/ structure
4. Classify existing 02-knowledge/ notes:

• If tags include research, summary, or reference in frontmatter → move to 04-resources/[same subfolder]
• If frontmatter has a source: field matching /research, /summarize, or /reading-notes → move to 04-resources/[same subfolder]
• Otherwise → keep in 03-knowledge/ (treat as synthesized content)
• Notes that cannot be automatically classified → list them and ask the user before moving

1. Verify 05-agent/MEMORY-INDEX.md exists; if not, create an empty MEMORY-INDEX.md with the standard frontmatter (total_active: 0, total_needs_review: 0, updated: YYYY-MM-DD)
2. Update onebrain.yml with all 8 keys:

``yaml folders: inbox: 00-inbox projects: 01-projects areas: 02-areas knowledge: 03-knowledge resources: 04-resources agent: 05-agent archive: 06-archive logs: 07-logs ``

1. Report: files moved to 04-resources/, files kept in 03-knowledge/, files needing manual review

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Subfolder Migration

Move existing flat notes into category-based subfolders (kebab-case, max 2 levels). Run this once after upgrading to a version of OneBrain that uses subfolders.

Step 1: Scan for Flat Notes

Find notes that are directly in a top-level folder (not already in a subfolder):

• [projects_folder]/*.md : glob top-level only (not [projects_folder]/**/*.md)
• [areas_folder]/*.md : glob top-level only
• [knowledge_folder]/*.md : glob top-level only
• [resources_folder]/*.md : glob top-level only
• ~~[logs_folder]/*-session-*.md~~ — Removed in v2.4.0. Session logs now live under [logs_folder]/session/YYYY/MM/; /update migration owns the 07-logs structure end-to-end. /reorganize no longer touches [logs_folder]/.

Legacy 07-logs structure guard (post-v2.4.0): before scanning anything else, check whether [logs_folder]/YYYY/MM/ contains any of *-session-*.md, *-checkpoint-*.md, or *-update-*.md files. If yes → abort immediately with the message: ⚠️ 07-logs structure outdated — run /update first to migrate, then re-run /reorganize. Do not proceed; do not touch any folder. The /update Step 0 migration owns this structure transition; running /reorganize on a half-migrated vault would leave session logs stranded outside session/.

Also check [archive_folder]/*.md for any flat archive files.

Exclude .gitkeep files.

Report: ────────────────────────────────────────────────────────────── 📁 Proposed Reorganization ────────────────────────────────────────────────────────────── 🗂️ [knowledgefolder]/ ({N} notes) 🗂️ [resourcesfolder]/ ({N} notes) 🗂️ [areasfolder]/ ({N} notes) 🗂️ [projectsfolder]/ ({N} notes) 🗂️ [archive_folder]/ ({N} archive files)

If nothing is found: ✅ Nothing to do — vault already organized into subfolders.

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Step 2: Propose Subfolder Assignments

For each note, analyze its content and frontmatter to suggest a subfolder:

For [knowledge_folder]/, [resources_folder]/, [areas_folder]/, and [projects_folder]/ notes:

• Read the file's title, tags, and first paragraph
• Suggest a kebab-case subfolder path (max 2 levels, e.g. programming/python, health/fitness)
• Group notes with the same suggested subfolder together

For [archive_folder]/ flat files:

• Use today's date for archiving: YYYY/MM
• Or read the note's created: frontmatter if present and use that date instead

Present the full migration plan:

──────────────────────────────────────────────────────────────
📁 Proposed Reorganization
──────────────────────────────────────────────────────────────
🗂️  {folder}/ ({N} notes)
  {Note name}          →  {subfolder}
  {Note name}          →  {subfolder}

🗂️  {folder}/ ({N} notes)
  {Note name}          →  {subfolder}
──────────────────────────────────────────────────────────────
{N} notes total · Proceed?

If more than 40 notes total, show the first 40 and add: (showing 40 of {N} — run /reorganize again to continue)

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Step 3: Let User Adjust

Say: > Does this look right? You can: > - Approve all : move everything as proposed > - Adjust a note : tell me the note name and where to put it instead > - Skip a note : tell me which ones to leave in place > - Cancel : do nothing

Wait for response. Apply any requested adjustments before proceeding.

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Step 4: Execute Moves

For each approved move:

1. Ensure the target subfolder exists ([target_folder]/[subfolder]). Most portable: node -e "require('fs').mkdirSync(process.argv[1], { recursive: true })" -- "[target_folder]/[subfolder]". Native shell forms also work: mkdir -p (Bash), New-Item -ItemType Directory -Force (PowerShell — never mkdir -p here), mkdir (cmd). Existing-directory errors are non-fatal.
2. Move the file from [source_path] to [target_path]. Use mv on Bash, Move-Item on PowerShell, move on cmd.
3. Confirm each move silently; report errors immediately

Process notes by folder (all knowledge, then resources, then areas, then projects, then archive).

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Step 5: Summary

Report: ✅ Moved {N} notes into subfolders.

• Moved N notes in [knowledge_folder]/ into N subfolders
• Moved N notes in [resources_folder]/ into N subfolders
• Moved N notes in [areas_folder]/ into N subfolders
• Moved N notes in [projects_folder]/ into N subfolders
• Moved N files in [archive_folder]/ into YYYY/MM folders
• Skipped N notes (left in place)

All existing wikilinks ([[Note Name]]) still work : Obsidian resolves links by filename, not path.

Want to run /connect to find new connections between your organized notes?

onebrain qmd reindex

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Step 6: Write Log Entry

Follow ../_shared/audit-log-format.md (canonical frontmatter, append-per-day algorithm, run-section heading, failure mode) with:

• Filename: YYYY-MM-DD-reorganize.md — one file per day. Applies whether the run was a Full Migration (5-folder → 8-folder), a Subfolder Migration, or both.
• Tags: [audit-log, reorganize]
• Skill: /reorganize
• Per-skill discriminator in frontmatter: mode: full | subfolder | both
• No-op runs: if the scan found nothing to do (already organized), skip writing — there is nothing to log.

Per-skill body template (canonical ## Run HH:MM heading; metadata in first bullet):

## Run HH:MM

- Mode: subfolder
- Files moved: N
- Folders created: M

### Files moved
- `03-knowledge/ai-thought.md` → `03-knowledge/ai/AI Thought.md`
- `03-knowledge/python.md` → `03-knowledge/dev/Python.md`
... (full list)

### Folders created
- `03-knowledge/ai/`, `03-knowledge/dev/`

### Wikilinks repaired
- N links updated across M notes (preserved targets via Obsidian)

---

Progress reporting

This skill is long-running. Emit a 1-line status update after each major step so the user can see progress in real time.

In-session format:

→ [step N/M] 

Examples:

→ [step 1/6] scanning flat notes...
→ [step 2/6] proposing subfolder structure...
→ [step 3/6] showing user diff preview...
→ [step 4/6] (awaiting confirmation)...
→ [step 5/6] moving files in batches...
→ [step 6/6] updating MEMORY-INDEX + wikilinks...

Rules:

• Emit one line per major step (NOT per sub-step or tool call)
• M = total steps known up front (count them before starting)
• Status lines use → [step N/M] prefix exactly so they're visually distinct from skill output
• Do NOT emit heartbeats for fast operations (< 5 seconds)

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Known Gotchas

• Wikilinks are path-independent in Obsidian. Moving files does NOT break [[Note Name]] links — Obsidian resolves by filename, not path. The skill already notes this, but it is the most common user concern; reassure proactively before executing moves.

• Full migration: classification of old 02-knowledge/ notes into 03-knowledge/ vs 04-resources/ is imperfect. Notes without explicit source frontmatter require judgment. When uncertain, err on the side of keeping notes in 03-knowledge/ — the user can always move them to 04-resources/ later via /consolidate.

• 40-note batch limit. If the vault has more than 40 flat notes, the skill shows the first 40 and offers to continue on the next run. Inform the user upfront if the vault is large.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: onebrain-ai
• Source: onebrain-ai/onebrain
• License: Apache-2.0
• Homepage: https://onebrain.run

Install and usage instructions live in the source repository linked above.