Gobi Migration Skill

Set up a new AI4PKM vault from scratch or migrate an existing vault to v0.0.29. The skill operates in two modes:

• Fresh Install: For new users — scaffolds the full vault structure, fetches all template files from GitHub, and runs onboarding
• Upgrade: For existing users — detects the current version, identifies which structural epochs are needed, and applies changes incrementally with full backup safety

Prerequisites

• GitHub CLI (gh) must be installed and authenticated — used to fetch template files
• Gobi CLI (gobi) must be installed for community features (spaces, brains, sessions)
  bashCopy

  npm install -g @gobi-ai/cli
  # or: brew tap gobi-ai/tap && brew install gobi
  

  Verify: gobi --version — see gobi-cli repo for details
• Template repo: jykim/ai4pkm-vault (public)
• This skill runs standalone in any user vault — it does NOT require being inside the template repo

When to Use

• User says "볼트 마이그레이션", "vault migration", or "migrate vault"
• User asks to upgrade an older vault to the latest template
• User cloned the template long ago and wants new Gobi features
• After vault-update (file-level) when structural changes are also needed
• User says "볼트 설정", "vault setup", or "set up vault"
• User says "새 볼트", "new vault", or "fresh install"
• User is in an empty directory and asks for help setting up a PKM vault

Quick Commands

"볼트 설정" / "setup vault" → Fresh install flow
"마이그레이션" / "migrate" → Upgrade flow (existing)
"마이그레이션 상태" / "migration status" → Detect version and show what's needed
"마이그레이션 검증" / "verify migration" → Run verification checklist

Relationship to vault-update

Recommended order: Run gobi-migration first (structural), then vault-update (file content).

Fetching Template Files from GitHub

When the migration needs a template file (prompt, base, config), fetch it from the repo:

# Fetch a single file's content (decoded from base64)
gh api "repos/jykim/ai4pkm-vault/contents/{path}?ref=main" -q '.content' | base64 -d

# Examples:
gh api "repos/jykim/ai4pkm-vault/contents/orchestrator.yaml?ref=main" -q '.content' | base64 -d
gh api "repos/jykim/ai4pkm-vault/contents/AGENTS.md?ref=main" -q '.content' | base64 -d
gh api "repos/jykim/ai4pkm-vault/contents/BRAIN.md?ref=main" -q '.content' | base64 -d
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Post%20Brain%20Update%20(PBU).md?ref=main" -q '.content' | base64 -d

# List directory contents
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts?ref=main" -q '.[].name'
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Bases?ref=main" -q '.[].name'

Important: Always wrap gh api URLs in double quotes. URLs containing ?ref=main will cause shell glob expansion errors if unquoted, potentially resulting in empty responses and 0-byte files.

Always fetch from main branch to get the latest template state. URL-encode spaces as %20 in paths.

Migration Flow

Step 0: Vault Root Detection

Before anything else, confirm we're operating in the correct directory.

Detection logic:

1. Check CWD for orchestrator.yaml or .obsidian/
2. If not found, walk parent directories (max 5 levels) looking for the same markers
3. Interpret results:

4. If ambiguous, ask user to confirm the vault root path
5. Warning: If CWD is inside the jykim/ai4pkm-vault template repo itself (check for .git/ remote pointing to jykim/ai4pkm-vault), warn the user — they probably want to operate in their own vault, not the template

Step 1: Mode Detection

After confirming the vault root, determine which flow to use.

Decision tree:

• Fresh Install: No orchestrator.yaml AND no _Settings_/ folder → run Fresh Install Flow
• Upgrade: orchestrator.yaml exists, version < 0.0.29 → run existing epoch-based migration
• Up-to-date: orchestrator.yaml exists, version == 0.0.29 → verify only, suggest vault-update for latest file content

For Upgrade mode, read orchestrator.yaml to determine the vault's current version.

Primary signal: version field

• "1.0" → original template (pre-epoch 1)
• "0.0.13" through "0.0.19" → epoch 1 done, needs epoch 2+
• "0.0.20" through "0.0.25" → epochs 1-2 done, needs epoch 3
• "0.0.26" through "0.0.29" → fully up to date

Fallback signals (if version is missing or "1.0"):

Step 2: Backup (Conditional)

Fresh Install: Skip backup — nothing to back up. Offer git init if the user wants version control from the start (this happens at the end of the fresh install flow).

Upgrade: This step is mandatory — migration must not proceed without user confirming their backup choice.

Present the following to the user:

마이그레이션을 시작하기 전에 백업을 권장합니다. 어떤 방식을 선호하시나요?
1. Git 리포지토리 초기화 (git init + initial commit) — 변경 이력 추적 가능
2. 압축 파일로 백업 (zip) — 간단한 스냅샷
3. 이미 백업했으므로 건너뛰기

Action by choice:

1. Git backup:

   • If .git/ already exists → create a pre-migration commit: git add -A && git commit -m "Pre-migration backup"
   • If no .git/ → git init && git add -A && git commit -m "Initial commit (pre-migration backup)"

2. Zip backup:

   • Create {vault_name}_backup_{timestamp}.zip in the parent directory of the vault
   bashCopy

   cd .. && zip -r "{vault_name}_backup_$(date +%Y%m%d_%H%M%S).zip" "{vault_name}/" && cd "{vault_name}"
   

3. Skip — user confirms they already have a backup

Step 3: Generate Plan & Confirm

Fresh Install: Show a summary of what will be created (directories, config files, prompts, skills) and ask for confirmation.

Upgrade: Based on detected version, determine which epochs apply. For each epoch, check every step's precondition and mark:

• ✅ Already done (precondition met)
• ⬜ TODO (needs to be applied)

Present the plan to the user. User can:

• Approve all
• Select specific epochs (upgrade only)
• Skip individual steps

Step 4: Execute

Fresh Install → run the Fresh Install Flow (see below)

Upgrade → apply changes epoch by epoch, step by step. Back up any modified files. Track progress in .gobi/migrations.yaml.

Step 5: Verify

Run the verification checklist to confirm everything is correct.

Step 6: Auto-invoke gobi-onboarding

After verification completes, automatically hand off to gobi-onboarding.

Fresh install → always full onboarding (BRAIN.md is a placeholder template):

마이그레이션이 완료됐어요! 이제 온보딩을 시작할게요.

→ Read _Settings_/Skills/gobi-onboarding/SKILL.md and begin full onboarding flow

Upgrade → route based on BRAIN.md state:

1. Check if BRAIN.md exists
   ├── No → "BRAIN.md가 없어요. 온보딩을 통해 프로필을 만들어볼까요?"
   │        → Read gobi-onboarding SKILL.md, invoke full flow
   └── Yes → Read BRAIN.md content
             ├── Template/placeholder (<100 words real content)
             │   → "마이그레이션이 완료됐어요! 프로필이 아직 기본 템플릿이에요. 온보딩을 시작할게요."
             │   → Read gobi-onboarding SKILL.md, invoke Step 4 (Community Onboarding)
             └── Rich content (>100 words, personalized)
                 → Check publish status (two-layer approach):
                   1. Read vaultSlug from .gobi/settings.yaml
                      └── If vaultSlug missing → "먼저 gobi init으로 볼트를 연결해주세요." → Suggest: gobi init
                   2. Primary: `gobi --json brain list-updates --mine --limit 1`
                      └── If data array non-empty → Already published (confirmed)
                   3. Fallback: `gobi --json brain search --query {vaultSlug}`
                      └── Parse JSON; check if any item in data has vaultSlug EXACTLY matching
                 ├── Already published (either check confirms)
                 │   → "마이그레이션이 완료됐어요! 프로필이 이미 커뮤니티에 공유돼 있어요."
                 │   → Suggest: gobi brain post-update (share what's new)
                 └── Not yet published (both checks negative)
                     → "마이그레이션이 완료됐어요! 프로필이 잘 갖춰져 있어요. 커뮤니티에 공유해볼까요?"
                     → Suggest: gobi brain publish

Fresh Install Flow

Creates a complete AI4PKM vault from scratch using the latest template files from GitHub.

FI-1: Scaffold Directories

Create the full directory structure:

mkdir -p _Settings_/{Prompts,Bases,Templates,Skills,Tasks,Guidelines,History,History/Ambient,History/Capture,Logs}
mkdir -p AI/{Analysis,Briefing,Canvas,Roundup,Summary,Writeup}
mkdir -p Ingest/{Clippings,Documents}
mkdir -p Journal
mkdir -p Topics
mkdir -p _Outbox_/BrainUpdates
mkdir -p .gobi
mkdir -p .claude

FI-2: Fetch Root Config Files

Fetch these files from the template repo into the vault root:

# Root configuration files
for file in orchestrator.yaml AGENTS.md CLAUDE.md GEMINI.md BRAIN.md BRAIN_PROMPT.md VAULTS.md README.md .gitignore; do
  gh api "repos/jykim/ai4pkm-vault/contents/${file}?ref=main" -q '.content' | base64 -d > "${file}"
done

Conflict handling: If any file already exists:

• Identical to template → skip silently
• Differs from template → ask user: overwrite / skip / merge
• orchestrator.yaml → always use merge logic (see Orchestrator Merge Rules)
• .gobi/settings.yaml → never overwrite, only add missing keys

FI-3: Fetch .gobi/ Config

# settings.yaml
gh api "repos/jykim/ai4pkm-vault/contents/.gobi/settings.yaml?ref=main" -q '.content' | base64 -d > .gobi/settings.yaml

# syncfiles
gh api "repos/jykim/ai4pkm-vault/contents/.gobi/syncfiles?ref=main" -q '.content' | base64 -d > .gobi/syncfiles

After creating settings.yaml, update user-specific values:

• claudePath — set via: which claude (or user's actual path)
• vaultSlug — will be set by gobi init during onboarding

If .gobi/settings.yaml already exists: Preserve as-is, only add missing keys by merging.

FI-4: Fetch Prompts, Bases, Templates

Use gh api directory listing to discover files dynamically (forward-compatible with new files added to the template):

# Fetch all prompts (use while-read to handle filenames with spaces)
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts?ref=main" -q '.[].name' | while IFS= read -r file; do
  encoded=$(echo "$file" | sed 's/ /%20/g')
  gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/${encoded}?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/${file}"
done

# Fetch all bases
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Bases?ref=main" -q '.[].name' | while IFS= read -r file; do
  encoded=$(echo "$file" | sed 's/ /%20/g')
  gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Bases/${encoded}?ref=main" -q '.content' | base64 -d > "_Settings_/Bases/${file}"
done

# Fetch all templates
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Templates?ref=main" -q '.[].name' | while IFS= read -r file; do
  encoded=$(echo "$file" | sed 's/ /%20/g')
  gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Templates/${encoded}?ref=main" -q '.content' | base64 -d > "_Settings_/Templates/${file}"
done

FI-5: Fetch Skills (Recursive)

Skills are organized in subdirectories. List each skill directory, then fetch its files:

# List skill directories (use while-read to handle names with spaces)
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Skills?ref=main" -q '.[] | select(.type=="dir") | .name' | while IFS= read -r skill_dir; do
  mkdir -p "_Settings_/Skills/${skill_dir}"
  encoded_dir=$(echo "$skill_dir" | sed 's/ /%20/g')
  # Fetch files in each skill directory
  gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Skills/${encoded_dir}?ref=main" -q '.[] | select(.type=="file") | .name' | while IFS= read -r file; do
    encoded_file=$(echo "$file" | sed 's/ /%20/g')
    gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Skills/${encoded_dir}/${encoded_file}?ref=main" -q '.content' | base64 -d > "_Settings_/Skills/${skill_dir}/${file}"
  done
done

FI-6: Create .claude/skills Symlink

mkdir -p .claude
ln -sf ../../_Settings_/Skills .claude/skills

FI-7: Optional Git Init

Offer to initialize version control:

볼트 설정이 완료됐어요! Git으로 버전 관리를 시작할까요?
1. Git 초기화 + 초기 커밋
2. 건너뛰기 (나중에 직접 설정)

If user chooses option 1:

git init
git add -A
git commit -m "Initial AI4PKM vault setup (v0.0.29)"

Fresh Install Conflict Handling

When a file already exists in the target directory during fresh install:

Epoch 1: Foundation (v1.0 → v0.0.13)

Adds Gobi 3.0 infrastructure: .gobi/ config, brain files, new orchestrator nodes, new prompts, folder restructuring.

1.0 Verify Prerequisites

Check: gh --version and gobi --version both succeed

Action: If gobi is not installed, install it before proceeding:

npm install -g @gobi-ai/cli
# or: brew tap gobi-ai/tap && brew install gobi

After install, run gobi init to authenticate and link the vault. This is required for community features (spaces, brain publish, sessions).

1.1 Remove Deprecated Orchestrator Fields

Check: orchestrator.yaml contains any of: stt_provider, stt_language, tts_provider, orchestrator_language, wakeword_enabled, wakeword_mode, manual_end_detection, periodic_processing, periodic_prompt, periodic_seconds, mic_gain

Action: Remove these fields from the orchestrator section. Back up file first.

1.2 Add Orchestrator Directory Fields

Check: orchestrator.yaml has chat_history_dir, ambient_recording_dir, file_extensions

Action: Add missing fields to the orchestrator section:

orchestrator:
  # ... existing fields ...
  chat_history_dir: _Settings_/History
  ambient_recording_dir: _Settings_/History/Ambient
  file_extensions:
    - .md
    - .pdf
    - .docx
    - .doc
    - .txt
    - .epub

1.3 Add Orchestrator Nodes

Check: For each node below, check if a node with that name exists in nodes:

Action: Add missing nodes:

  - type: agent
    name: Extract Document to Markdown (EDM)
    input_path: Ingest/Documents
    output_path: AI/Summary
    executor: claude_code
    input_type: new_file
    input_pattern: "*.pdf|*.docx|*.doc|*.txt|*.epub"
    trigger_exclude_pattern: "*.md"
    output_naming: "{title}.md"
    enabled: true
  - type: agent
    name: Generate Daily Roundup (GDR)
    cron: 0 4 * * *
    output_path: AI/Roundup
  - type: agent
    name: Topic Index Update (TIU)
    cron: 30 4 * * *
    input_path: AI/Roundup
    output_path: Topics
  - type: agent
    name: Ambient Canvas Brainstorming (ACB)
    input_path: _Settings_/History/Ambient
    output_path: AI/Canvas
    input_type: new_file
    output_naming: "{datetime} {title}.canvas"
    enabled: true

1.4 Create .gobi/ Directory and Settings

Check: .gobi/settings.yaml exists

⚠️ Never overwrite existing server-related .gobi/ files.

Action:

• If .gobi/settings.yaml does NOT exist → Create .gobi/ directory, fetch template, then prompt user to customize:

  bashCopy

  mkdir -p .gobi
  gh api "repos/jykim/ai4pkm-vault/contents/.gobi/settings.yaml?ref=main" -q '.content' | base64 -d > .gobi/settings.yaml
  

  Then update user-specific values:

  • vaultSlug — will be set by gobi init
  • claudePath — set to user's actual Claude CLI path (e.g., which claude)

• If .gobi/settings.yaml already exists → Preserve as-is. Only add missing keys by merging (do not replace). Compare with template and add any keys that don't exist in the user's file.

Default template content:

vaultSlug: ai4pkm-vault
selectedSpaceSlug: cmds
orchestratorEnabled: true
voiceSettings:
  primaryLanguage: ko
  secondaryLanguage: en
  llmProvider: claude-cli
  llmConfig:
    cli:
      claudePath: /usr/local/bin/claude

Note: User should run gobi init to properly set vaultSlug, and update claudePath to their actual path.

1.5 Create .gobi/syncfiles

Check: .gobi/syncfiles exists

⚠️ Never overwrite existing server-related .gobi/ files.

Action:

• If .gobi/syncfiles does NOT exist → Create from template:
  bashCopy

  gh api "repos/jykim/ai4pkm-vault/contents/.gobi/syncfiles?ref=main" -q '.content' | base64 -d > .gobi/syncfiles
  

• If .gobi/syncfiles already exists → Skip entirely with message: "기존 syncfiles를 유지합니다"

Default content (for new creation only):

/BRAIN.jpg
/BRAIN.md
/BRAIN_PROMPT.md

1.6 Create BRAIN.md

Check: BRAIN.md exists in vault root

Action: If BRAIN.md doesn't exist, defer to gobi-onboarding skill Step 1 for interactive profile creation rather than writing a placeholder template. The onboarding flow creates a personalized BRAIN.md through conversation, which is far more valuable than a generic template.

Fallback (if onboarding is not available or user prefers manual setup): Fetch template from repo:

gh api "repos/jykim/ai4pkm-vault/contents/BRAIN.md?ref=main" -q '.content' | base64 -d > BRAIN.md

Then user should customize. Template content:

---
title: "홍길동의 Second Brain"
description: "의적 홍길동 — 전쟁사·전략/전술·무기·정보 수집 전문"
thumbnail: "[[BRAIN.jpg]]"
prompt: "[[BRAIN_PROMPT.md]]"
tags:
  - profile
  - second-brain
created: 2024-01-01 00:00:00
---

## Welcome to My Second Brain

**홍길동** | 의적

### 전문 분야
- 전쟁사 — 역사 속 전쟁의 원인, 전개, 결과 분석
- 전략/전술 — 군사 전략과 전투 전술 연구
- 무기 — 고대부터 현대까지 무기 체계

### 핵심 역량
- 정보 수집 — 의적 활동을 위한 정보 수집과 분석

### 목표
- 지식 구축 — 전쟁사와 전략/전술 관련 지식을 체계적으로 정리

Note: User should customize name, description, expertise, and goals to match their profile.

1.7 Create BRAIN_PROMPT.md

Check: BRAIN_PROMPT.md exists in vault root

Action: Fetch from repo:

gh api "repos/jykim/ai4pkm-vault/contents/BRAIN_PROMPT.md?ref=main" -q '.content' | base64 -d > BRAIN_PROMPT.md

Template content:

## Rules of Engagement
- Use [[BRAIN.md]] and files linked from there to answer questions
  - Minimize the use of internal knowledge
  - Answer should be grounded by user's documents
- Adjust the tone / language to the person asking
- Speak as if you're the owner of this brain
  - When asked about your identity, make clear you're AI agent representing the owner
- Invite to connect the owner himself if the question is outside your scope

1.8 Create VAULTS.md

Check: VAULTS.md exists in vault root

Action: Fetch from repo:

gh api "repos/jykim/ai4pkm-vault/contents/VAULTS.md?ref=main" -q '.content' | base64 -d > VAULTS.md

Template content:

---
description: Vault registry for ai4pkm-vault
---

# Vault Registry

## Registered Vaults

### CV2601 (AI4PKM Community Vault)

| Property    | Value                        |
| ----------- | ---------------------------- |
| ID          | `CV2601`                     |
| Path        | [TBA]                        |
| Type        | `community`                  |
| Role        | `sub`                        |
| Description | AI4PKM 커뮤니티 볼트 - 지식 공유 및 Q&A |
| Access      | `read-write`                 |

#### Personal Vault Access Rules (for Community Prompts)

커뮤니티 프롬프트가 개인 볼트 콘텐츠를 읽을 때의 접근 규칙.

| Type      | Folders    |
| --------- | ---------- |
| Blacklist | `Journal/` |

---

### [Vault Name] (Template)

| Property | Value |
|----------|-------|
| ID | `` |
| Path | `` |
| Type | `` |
| Role | `` |
| Description | |
| Access | `` |

1.9 Create Required Folders

Check: Each folder exists

Action: Create missing folders:

• _Settings_/History/
• _Settings_/History/Ambient/
• Ingest/Documents/
• AI/Canvas/
• AI/Roundup/
• _Outbox_/

1.10 Add Skills Symlink

Check: .claude/skills symlink exists pointing to _Settings_/Skills

Action: Create symlink:

mkdir -p .claude
ln -sf ../../_Settings_/Skills .claude/skills

1.11 Add New Prompts (DDO, ICB, DRB, EDM, ACB)

Check: These prompt files exist in _Settings_/Prompts/:

• Daily Downloads Organizer (DDO).md
• Interactive Canvas Brainstorm (ICB).md
• Daily Research Briefing (DRB).md
• Extract Document to Markdown (EDM).md
• Ambient Canvas Brainstorming (ACB).md

Action: Fetch each missing prompt from GitHub:

# Example for each prompt (URL-encode spaces as %20):
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Daily%20Downloads%20Organizer%20(DDO).md?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/Daily Downloads Organizer (DDO).md"
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Interactive%20Canvas%20Brainstorm%20(ICB).md?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/Interactive Canvas Brainstorm (ICB).md"
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Daily%20Research%20Briefing%20(DRB).md?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/Daily Research Briefing (DRB).md"
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Extract%20Document%20to%20Markdown%20(EDM).md?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/Extract Document to Markdown (EDM).md"
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Ambient%20Canvas%20Brainstorming%20(ACB).md?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/Ambient Canvas Brainstorming (ACB).md"

1.12 Remove Deprecated Prompts

Check: These files do NOT exist in _Settings_/Prompts/:

• Personal Brain Chat (PBC).md
• Create Topic Page (CTP).md

Action: If they exist, back up and remove them (they were replaced by ICB and TIU respectively).

1.13 Update Version

Action: Set version: "0.0.13" in orchestrator.yaml (only if all steps above complete).

Epoch 2: Capture (v0.0.13 → v0.0.20)

Adds capture infrastructure, PBU prompt, new bases, Outbox, and AGENTS.md expansion.

2.1 Add Captures Configuration

Check: orchestrator.yaml contains captures_dir

Action: Add to the orchestrator section:

orchestrator:
  # ... existing fields ...
  captures_dir: _Settings_/History/Capture
  capture_prompt_path: _Settings_/Prompts/Ambient Canvas Brainstorming (ACB).md

2.2 Create Capture Folders

Check: _Settings_/History/Capture/ exists

Action: Create the folder:

mkdir -p "_Settings_/History/Capture"

2.3 Add PBU Prompt

Check: _Settings_/Prompts/Post Brain Update (PBU).md exists

Action: Fetch from GitHub:

gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Prompts/Post%20Brain%20Update%20(PBU).md?ref=main" -q '.content' | base64 -d > "_Settings_/Prompts/Post Brain Update (PBU).md"

2.4 Add New Bases

Check: These base files exist in _Settings_/Bases/:

• Participants.base
• Publish.base
• Skills.base

Action: Fetch each from GitHub:

gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Bases/Participants.base?ref=main" -q '.content' | base64 -d > "_Settings_/Bases/Participants.base"
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Bases/Publish.base?ref=main" -q '.content' | base64 -d > "_Settings_/Bases/Publish.base"
gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Bases/Skills.base?ref=main" -q '.content' | base64 -d > "_Settings_/Bases/Skills.base"

2.5 Create BrainUpdates Outbox

Check: _Outbox_/BrainUpdates/ folder exists

Action: Create the folder:

mkdir -p "_Outbox_/BrainUpdates"

2.6 Expand AGENTS.md

Check: AGENTS.md contains sections for Skills, Search over files, and Gobi Space Features

Action: Fetch latest AGENTS.md from GitHub template and do a section-level merge:

gh api "repos/jykim/ai4pkm-vault/contents/AGENTS.md?ref=main" -q '.content' | base64 -d > /tmp/AGENTS_latest.md

Then compare sections and add any missing ones while preserving user customizations. See AGENTS.md Merge Rules below.

2.7 Update Version

Action: Set version: "0.0.20" in orchestrator.yaml.

Epoch 3: Polish (v0.0.20 → v0.0.29)

Version bump, AGENTS.md Gobi sections, CLAUDE.md refinements, onboarding skill updates.

3.1 Update AGENTS.md Gobi Sections

Check: AGENTS.md contains "Gobi Space Features" section with gobi-cli references

Action: If missing, add the Gobi Space Features section from the latest template (see AGENTS.md merge rules).

3.2 Update CLAUDE.md

Check: CLAUDE.md references AGENTS.md for generic rules

Action: Fetch latest CLAUDE.md from GitHub and compare. If the user has a monolithic CLAUDE.md (all rules inline), suggest splitting into CLAUDE.md (agent-specific) + AGENTS.md (generic). See CLAUDE.md Merge Rules below.

3.3 Update Onboarding Skill

Check: _Settings_/Skills/gobi-onboarding/SKILL.md exists and is recent

Action: Fetch latest from GitHub. The onboarding skill changes frequently, so always pull the current version:

# Fetch the entire gobi-onboarding skill directory
for file in $(gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Skills/gobi-onboarding?ref=main" -q '.[].name'); do
  gh api "repos/jykim/ai4pkm-vault/contents/_Settings_/Skills/gobi-onboarding/${file}?ref=main" -q '.content' | base64 -d > "_Settings_/Skills/gobi-onboarding/${file}"
done

3.4 Update Version to Target

Action: Set version: "0.0.29" in orchestrator.yaml.

3.5 Add id/name Fields

Check: orchestrator.yaml has id and name fields at root level

Action: Add if missing:

id: ai4pkm_vault
name: ai4pkm_vault

Orchestrator Merge Rules

When merging orchestrator.yaml, follow these rules:

Preserve

• User-custom nodes: Any node name not in the template → keep as-is
• User-modified fields on template nodes: If user changed output_path, cron, enabled, etc. on a template node → keep user's values
• Pollers: User's poller configuration is always preserved

Add

• Missing template nodes: Match by name field. If a template node name is not found in user's config, add it
• Missing orchestrator fields: Add new fields (e.g., captures_dir) without removing existing ones

Remove

• Deprecated fields: Remove fields listed in epoch 1.1 (STT/TTS/wakeword settings)
• Deprecated nodes: None currently — no template nodes have been removed

Version

• Only update version field after all epoch steps are verified

AGENTS.md Merge Rules

AGENTS.md is section-based (H2 headers). Merge strategy:

1. Parse both files into sections (split on ## headers)
2. For each section in template:
   • If section header exists in user's file → keep user's version (they may have customized)
   • If section header is missing → add it at the appropriate position
3. For each section only in user's file → keep it (user-added content)
4. Flag conflicts: If a section exists in both but content differs significantly, show both and let user choose

Key sections to ensure exist (as of v0.0.29):

• ## Core Mission & Principles
• ## Prompts & Workflows
• ## Skills
• ## Search over files
• ## 📝 Content Creation Requirements
• ## 🔄 Additional Principles
• ## Quality Standards
• ## Multi-Vault Operations
• ## Gobi Space Features

CLAUDE.md Merge Rules

CLAUDE.md should be agent-specific (Claude Code only), referencing AGENTS.md for generic rules.

1. Check structure: If CLAUDE.md has generic rules that belong in AGENTS.md, suggest moving them
2. Ensure reference: First line after frontmatter should be: **All generic rules are defined in @AGENTS.md
3. Keep agent-specific sections: Task Management, Version Control, Tool Usage, etc.
4. Add missing sections: Compare with template and add any missing Claude-specific sections

Target orchestrator.yaml Structure (v0.0.29)

version: 0.0.29
orchestrator:
  prompts_dir: _Settings_/Prompts
  tasks_dir: _Settings_/Tasks
  logs_dir: _Settings_/Logs
  skills_dir: .claude/skills
  bases_dir: _Settings_/Bases
  chat_history_dir: _Settings_/History
  ambient_recording_dir: _Settings_/History/Ambient
  system_prompt_file: _Settings_/Prompts/Real-time Voice Assistant (RVA).md
  max_concurrent: 3
  poll_interval: 1
  file_extensions:
    - .md
    - .pdf
    - .docx
    - .doc
    - .txt
    - .epub
  captures_dir: _Settings_/History/Capture
  capture_prompt_path: _Settings_/Prompts/Ambient Canvas Brainstorming (ACB).md
defaults:
  executor: claude_code
  timeout_minutes: 30
  max_parallel: 3
  task_create: true
  task_priority: medium
  task_archived: false
nodes:
  - type: agent
    name: Enrich Ingested Content (EIC)
    input_path: Ingest/Clippings
    output_path: AI/Summary
    output_type: new_file
  - type: agent
    name: Extract Document to Markdown (EDM)
    input_path: Ingest/Documents
    output_path: AI/Summary
    executor: claude_code
    input_type: new_file
    input_pattern: "*.pdf|*.docx|*.doc|*.txt|*.epub"
    trigger_exclude_pattern: "*.md"
    output_naming: "{title}.md"
    enabled: true
  - type: agent
    name: Generate Daily Roundup (GDR)
    cron: 0 4 * * *
    output_path: AI/Roundup
  - type: agent
    name: Topic Index Update (TIU)
    cron: 30 4 * * *
    input_path: AI/Roundup
    output_path: Topics
  - type: agent
    name: Ambient Canvas Brainstorming (ACB)
    input_path: _Settings_/History/Ambient
    output_path: AI/Canvas
    input_type: new_file
    output_naming: "{datetime} {title}.canvas"
    enabled: true
  # User-custom nodes are preserved here
id: ai4pkm_vault
name: ai4pkm_vault

Migration Tracking

Track applied migrations in .gobi/migrations.yaml:

migrations:
  - epoch: 1
    name: Foundation
    applied_at: 2026-03-18T10:00:00-07:00
    from_version: "1.0"
    to_version: "0.0.13"
    steps_applied: [1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 1.10, 1.11, 1.12, 1.13]
    steps_skipped: []
  - epoch: 2
    name: Capture
    applied_at: 2026-03-18T10:05:00-07:00
    from_version: "0.0.13"
    to_version: "0.0.20"
    steps_applied: [2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7]
    steps_skipped: []
  - epoch: 3
    name: Polish
    applied_at: 2026-03-18T10:10:00-07:00
    from_version: "0.0.20"
    to_version: "0.0.29"
    steps_applied: [3.1, 3.2, 3.3, 3.4, 3.5]
    steps_skipped: []

For fresh installs, track as:

migrations:
  - epoch: fresh_install
    name: Fresh Install
    applied_at: 2026-03-18T10:00:00-07:00
    from_version: null
    to_version: "0.0.29"
    steps_applied: [FI-1, FI-2, FI-3, FI-4, FI-5, FI-6, FI-7]
    steps_skipped: []

Verification Checklist

After migration completes, verify:

Prerequisites

• gh --version succeeds (GitHub CLI installed)
• gobi --version succeeds (Gobi CLI installed)
• gobi auth status shows authenticated

Structure

• .gobi/settings.yaml exists with vaultSlug and selectedSpaceSlug
• .gobi/syncfiles exists with brain file paths
• BRAIN.md exists with valid YAML frontmatter
• BRAIN_PROMPT.md exists
• VAULTS.md exists
• .claude/skills symlink points to _Settings_/Skills

Folders

• _Settings_/History/ exists
• _Settings_/History/Ambient/ exists
• _Settings_/History/Capture/ exists
• Ingest/Documents/ exists
• AI/Canvas/ exists
• AI/Roundup/ exists
• _Outbox_/ exists
• _Outbox_/BrainUpdates/ exists

Orchestrator

• version is 0.0.29
• No deprecated fields (STT/TTS/wakeword)
• Has chat_history_dir, ambient_recording_dir, file_extensions
• Has captures_dir, capture_prompt_path
• Has nodes: EIC, EDM, GDR, TIU, ACB
• Has id and name at root level
• User-custom nodes preserved

Prompts

• DDO, ICB, DRB, EDM, ACB, PBU prompts exist
• Deprecated prompts (PBC, CTP) removed

Bases

• Participants.base, Publish.base, Skills.base exist

Config Files

• AGENTS.md has all required sections
• CLAUDE.md references AGENTS.md

Safety Rules

1. Non-destructive: Always back up modified files as {name}.bak.{timestamp} before changes
2. No user content deletion: Never modify files in Ingest/, Journal/, Topics/, AI/ (except creating folders)
3. Incremental: Apply one epoch at a time, verify before proceeding
4. Idempotent: Each step checks preconditions — running migration twice is safe
5. User approval: Always show plan before executing; never auto-apply
6. Preserve customizations: User-added nodes, settings, and content are never removed
7. Track everything: Log all changes to .gobi/migrations.yaml
8. Protected files: Never overwrite existing .gobi/ server-related files (syncfiles, settings.yaml, sync_state_v3.db) — these contain user-specific configuration and sync state. Only create if missing; merge missing keys if needed.
9. Backup required: Always offer backup (git commit or zip) before starting migration (see Step 2)
10. Quote all URLs: All gh api URL arguments must be wrapped in double quotes to prevent shell glob expansion of ? characters
11. Never silently overwrite: During fresh install, if an existing file differs from the template, always ask the user before overwriting (overwrite / skip / merge)
12. Dynamic file discovery: Use gh api directory listing to discover template files rather than hardcoding filenames — this ensures forward-compatibility when new files are added to the template

Troubleshooting

"orchestrator.yaml has no version field"

This means the vault predates versioning. Treat as v1.0 and start from epoch 1.

"Migration says TODO but the file already exists"

The precondition check may be looking for specific content, not just file existence. Check the step details for what exactly is being verified.

"I have custom nodes that disappeared"

This should not happen — the merge preserves all user-custom nodes. Check .gobi/migrations.yaml for what was applied and restore from orchestrator.yaml.bak.*.

"AGENTS.md merge conflict"

If sections differ between user's file and template, the migration will flag the conflict and show both versions. Choose which to keep, or manually merge.

"vault-update vs migration — which first?"

Run gobi-migration first for structural changes, then vault-update for latest file content. Migration sets up the structure; vault-update fills in the latest prompt/skill content.

"Can I roll back?"

All modified files have .bak.{timestamp} backups. To roll back an epoch:

1. Restore backed-up files
2. Remove the epoch entry from .gobi/migrations.yaml
3. Revert the version in orchestrator.yaml

"Vault root not detected"

The skill looks for orchestrator.yaml or .obsidian/ in the current directory and up to 5 parent directories. If neither is found:

• Confirm you're in the right directory
• For fresh install: any empty directory is fine — the skill will create everything
• For upgrade: navigate to your vault root first, or specify the path when prompted

"gh api rate limit during fresh install"

Fresh install makes many API calls to fetch all template files. If you hit GitHub's rate limit:

• Wait a few minutes and retry
• Use a GitHub Personal Access Token (PAT) for higher rate limits: gh auth login --with-token
• The skill tracks progress, so retrying will skip already-fetched files

"Fresh install in non-empty directory"

If the target directory already has files, the skill uses conflict handling:

• Files identical to the template are skipped silently
• Files that differ trigger a prompt: overwrite / skip / merge
• User content directories (Journal/, Topics/, etc.) are never touched
• .gobi/settings.yaml is never overwritten — only missing keys are added