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 vault.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 vault.yml is missing folders.areas.

1. Create new folders: 02-areas/, 04-resources/, 05-agent/context/, 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
5. Write README.md into each new root folder (content from .claude/plugins/onebrain/skills/onboarding/SKILL.md Step 10b)
6. Update vault.yml with all 8 keys:

   method: onebrain
   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
   

7. 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):

• 01-projects/*.md : glob top-level only (not 01-projects/**/*.md)
• 02-areas/*.md : glob top-level only
• 03-knowledge/*.md : glob top-level only
• 04-resources/*.md : glob top-level only
• 07-logs/*.md : flat session log files not yet in a YYYY/MM/ subfolder

Also check 06-archive/*.md for any flat archive files.

Exclude .gitkeep files.

Report:

Found N notes to organize:

• 03-knowledge/: N notes
• 04-resources/: N notes
• 02-areas/: N notes
• 01-projects/: N notes
• 07-logs/: N session logs
• 06-archive/: N archive files

If nothing is found, say:

Your vault is already organized into subfolders : nothing to do!

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Step 2: Propose Subfolder Assignments

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

For 03-knowledge/, 04-resources/, 02-areas/, and 01-projects/ 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 07-logs/ session log files:

• Extract YYYY and MM from the filename (YYYY-MM-DD-session-NN.md)
• Suggest YYYY/MM as the subfolder

For 06-archive/ 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 as a table:

## Proposed Reorganization

### 03-knowledge/ (N notes)
| Note | → Subfolder |
|------|------------|
| Machine Learning.md | → technology/ai |
| Sleep Optimization.md | → health |

### 04-resources/ (N notes)
| Note | → Subfolder |
|------|------------|
| Python Basics.md | → programming/python |

### 01-projects/ (N notes)
| Note | → Subfolder |
|------|------------|
| Website Redesign.md | → web-development |

### 07-logs/ (N session logs)
| File | → Subfolder |
|------|------------|
| 2026-01-15-session-01.md | → 2026/01 |
| 2026-02-03-session-01.md | → 2026/02 |

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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. Create the subfolder if it doesn't exist (use mkdir -p [target_folder]/[subfolder])
2. Move the file: mv "[source_path]" "[target_path]"
3. Confirm each move silently; report errors immediately

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

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Step 5: Summary

Report:

Reorganization complete!

• Moved N notes in 03-knowledge/ into N subfolders
• Moved N notes in 04-resources/ into N subfolders
• Moved N notes in 02-areas/ into N subfolders
• Moved N notes in 01-projects/ into N subfolders
• Moved N session logs in 07-logs/ into YYYY/MM folders
• Moved N files in 06-archive/ 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?