thoth-plugin 1.2.0 → 1.2.2

package/dist/defaults/skill/_legacy/link-retrofit/SKILL.md

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+---
+name: link-retrofit
+description: Proactively discovers and suggests cross-references between knowledge base files. Uses rule-based confidence tiers to ensure high-quality links. Can scan entire KB or specific paths.
+---
+
+# Link Retrofit Skill
+
+You are the **Knowledge Base Linker**. Your role is to proactively discover missing cross-references between files and suggest (or apply) bidirectional `[[wikilinks]]`.
+
+**Philosophy**: Links should be **high-signal, not exhaustive**. A link exists because following it provides value to the reader. We prefer fewer, high-confidence links over many weak ones.
+
+---
+
+## Operating Modes
+
+| Mode | Command | Action | Writes |
+|------|---------|--------|--------|
+| **Scan** | `/link-retrofit` or `/link-retrofit scan [path]` | Discover and report suggestions | No |
+| **Plan** | `/link-retrofit plan [path]` | Generate `kernel/link-plan.md` | Plan file only |
+| **Apply** | `/link-retrofit apply` | Apply approved links from plan | Yes (KB files) |
+
+---
+
+## Confidence Tiers (CRITICAL)
+
+**Do NOT ask the LLM for confidence scores.** Instead, use evidence-based tiers:
+
+| Tier | Confidence | Evidence Required | Action |
+|------|------------|-------------------|--------|
+| **CERTAIN** | 99% | Explicit name match in content → file exists with that name | Auto-suggest |
+| **STRONG** | 90% | 2+ signals present (see Signal Matrix below) | Suggest with review |
+| **MEDIUM** | 70% | 1 signal present | List only (optional) |
+| **WEAK** | <50% | Semantic similarity only, no structural evidence | Ignore |
+
+### Signal Matrix
+
+| Signal | Description | Weight |
+|--------|-------------|--------|
+| **Name Mention** | File content contains exact name that matches another file's title/H1 | +40 |
+| **Related Frontmatter** | `related: [file]` exists but no `[[link]]` in body | +40 |
+| **Same Project Folder** | Both files in same `projects/X/` subfolder | +20 |
+| **Shared Tags** | ≥2 overlapping tags in frontmatter | +20 |
+| **Reports-To Chain** | Person A's file mentions Person B in hierarchy context | +30 |
+| **Project Assignment** | Person file mentions project name that exists as file | +30 |
+| **Reciprocal Gap** | File A links to B, but B doesn't link back to A | +35 |
+
+**Scoring**:
+- CERTAIN: Name Mention with exact file match
+- STRONG: Score ≥ 60
+- MEDIUM: Score 30-59
+- WEAK: Score < 30
+
+---
+
+## Mode 1: Scan (Default)
+
+### Step 1: Build File Index
+
+For each `.md` file in the target path, extract:
+
+```yaml
+file_index:
+  - path: "work/Team/chirag-deora.md"
+    title: "Chirag Deora"           # From H1 or frontmatter summary
+    type: "person"                   # From frontmatter
+    hemisphere: "work"
+    tags: []
+    related: []                      # From frontmatter
+    existing_links: ["[[project-x]]"] # Already present wikilinks
+    mentions: ["Entra ID", "IAM"]    # Key terms in content
+```
+
+### Step 2: Build Entity Registry
+
+Create a lookup of linkable entities:
+
+```yaml
+entity_registry:
+  people:
+    - name: "Chirag Deora"
+      file: "work/Team/chirag-deora.md"
+      aliases: ["Chirag"]            # First name as alias
+    - name: "Joanna Thomas"
+      file: "work/Stakeholders/joanna-thomas.md"
+      aliases: ["Joanna"]
+  projects:
+    - name: "Okta Migration"
+      file: "work/projects/okta-migration.md"
+      aliases: ["Okta Migration Assessment"]
+  # ... etc
+```
+
+### Step 3: Scan for Missing Links
+
+For each file, check:
+
+1. **Name Mentions**: Does content mention any entity name (or alias) that isn't already linked?
+2. **Related Field**: Does `related:` frontmatter reference files not linked in body?
+3. **Reciprocal Links**: Does this file link to others that don't link back?
+4. **Project Context**: For person files, are mentioned projects linked?
+5. **Hierarchy Context**: For "Reports To" mentions, is the person linked?
+
+### Step 4: Score and Tier
+
+For each potential link, calculate score and assign tier.
+
+### Step 5: Output Report
+
+```markdown
+## Link Retrofit Scan Report
+
+**Scanned**: {timestamp}
+**Path**: {scanned_path}
+**Files Analyzed**: {count}
+
+### Summary
+| Tier | Count | Action |
+|------|-------|--------|
+| CERTAIN | X | Ready to apply |
+| STRONG | X | Review recommended |
+| MEDIUM | X | Optional |
+
+---
+
+### CERTAIN Tier (Auto-Apply Candidates)
+
+| Source File | Add Link | Reason |
+|-------------|----------|--------|
+| `work/Stakeholders/joanna-thomas.md` | `[[bianca-stef]]` | Name "Bianca Stef" mentioned in "Reports To" |
+| `work/Stakeholders/joanna-thomas.md` | `[[vasco-taveira]]` | Name "Vasco Taveira" mentioned in context |
+
+### STRONG Tier (Review Recommended)
+
+| Source File | Add Link | Reason | Score |
+|-------------|----------|--------|-------|
+| `work/Team/chirag-deora.md` | `[[okta-migration]]` | Mentions "Entra ID" (related project) | 65 |
+
+### Reciprocal Gaps
+
+| File A Links To | But Missing Backlink |
+|-----------------|---------------------|
+| `[[chirag-deora]]` in project-x.md | chirag-deora.md → project-x.md |
+
+---
+
+### Statistics
+- Total potential links found: X
+- CERTAIN: X (Y% of total)
+- STRONG: X
+- MEDIUM: X (excluded from plan)
+```
+
+---
+
+## Mode 2: Plan
+
+### Step 1: Run Scan
+
+Execute Mode 1 to get current suggestions.
+
+### Step 2: Generate Link Plan
+
+Create `kernel/link-plan.md`:
+
+```markdown
+---
+type: link-plan
+created: YYYY-MM-DD
+status: pending
+---
+
+# Link Retrofit Plan
+
+Generated: {timestamp}
+Scanned Path: {path}
+
+## Execution Summary
+
+| Tier | Links | Files Affected |
+|------|-------|----------------|
+| CERTAIN | X | Y |
+| STRONG | X | Y |
+| **Total** | X | Y |
+
+---
+
+## Phase 1: CERTAIN Links (Auto-Apply)
+
+These links have explicit name matches and are safe to apply.
+
+### 1.1 Person Name Links
+
+| File | Line | Current Text | Suggested Edit |
+|------|------|--------------|----------------|
+| `joanna-thomas.md` | 20 | "Reports To: Bianca Stef" | "Reports To: [[bianca-stef\|Bianca Stef]]" |
+| `joanna-thomas.md` | 21 | "Vasco Taveira is on leave" | "[[vasco-taveira\|Vasco Taveira]] is on leave" |
+
+### 1.2 Reciprocal Links
+
+| File | Add to Section | Link |
+|------|---------------|------|
+| `chirag-deora.md` | Related Links | `[[project-x]]` |
+
+---
+
+## Phase 2: STRONG Links (Review Required)
+
+These links have multiple signals but benefit from human review.
+
+| File | Suggested Link | Reason | Approve? |
+|------|---------------|--------|----------|
+| `okta-migration.md` | `[[chirag-deora]]` | Mentions Entra ID (Chirag's domain) | [ ] |
+
+---
+
+## Execution Checklist
+
+- [ ] Phase 1.1: Apply person name links
+- [ ] Phase 1.2: Apply reciprocal links
+- [ ] Phase 2: Review and apply strong links
+- [ ] Re-run scan to verify
+
+---
+
+*Run `/link-retrofit apply` to execute this plan.*
+```
+
+---
+
+## Mode 3: Apply
+
+**CRITICAL: This mode modifies files. Require explicit approval.**
+
+### Pre-Flight Checks
+
+1. Verify `kernel/link-plan.md` exists and is recent (< 24 hours)
+2. If no plan exists, prompt: "Run `/link-retrofit plan` first"
+3. Confirm user wants to proceed
+
+### Execution Protocol
+
+#### For Each Link in Plan:
+
+1. **Read** the source file
+2. **Locate** the text to modify (use line number from plan)
+3. **Show** the proposed edit:
+   ```
+   File: work/Stakeholders/joanna-thomas.md
+   Line 20: "Reports To: Bianca Stef"
+        →   "Reports To: [[bianca-stef|Bianca Stef]]"
+   ```
+4. **Batch by tier**: 
+   - CERTAIN: "Apply all X CERTAIN links? (yes/no)"
+   - STRONG: Show each, ask individually
+
+#### Link Insertion Rules
+
+**For name mentions in prose**:
+```markdown
+# Before
+Reports To: Bianca Stef
+
+# After  
+Reports To: [[bianca-stef|Bianca Stef]]
+```
+
+**For adding related links section** (if no existing links):
+```markdown
+# Add at end of file, before any --- separator
+
+## Related
+
+- [[linked-file]]
+```
+
+**For reciprocal links**:
+Add to the "Related" section, or create one if missing.
+
+### Post-Execution
+
+1. Log changes to `kernel/memory/link-retrofit-log.md`
+2. Update `kernel/link-plan.md` status to `completed`
+3. Report summary: "Applied X links across Y files"
+
+---
+
+## Technical Constraints
+
+### Safety Rules
+
+1. **NEVER** modify content meaning — only add link syntax around existing text
+2. **NEVER** add links inside code blocks or frontmatter
+3. **NEVER** create duplicate links (check if link already exists)
+4. **ALWAYS** use aliased links for names: `[[file-name|Display Name]]`
+5. **ALWAYS** preserve original text when wrapping with link
+
+### Entity Matching Rules
+
+**Exact Match Required for CERTAIN**:
+- "Chirag Deora" → `chirag-deora.md` ✓
+- "Chirag" alone → Only if unambiguous (no other Chirag exists)
+- "CD" or initials → Never auto-link
+
+**Case Sensitivity**:
+- Match is case-insensitive for detection
+- Preserve original case in display text
+
+**Avoid False Positives**:
+- Skip common words that happen to be names (e.g., "Will" as future tense vs person)
+- Skip mentions inside quotes that might be external references
+- Skip mentions in "Example:" or template sections
+
+### File Types to Process
+
+| Include | Exclude |
+|---------|---------|
+| `work/**/*.md` | `**/templates/**` |
+| `life/**/*.md` | `**/Archive/**` |
+| `coding/**/*.md` | `**/_index.md` |
+| `kernel/knowledge/**/*.md` | `**/README.md` |
+
+---
+
+## Integration with Gardener
+
+This skill complements `/gardener`:
+
+| Gardener | Link Retrofit |
+|----------|---------------|
+| Finds **broken** links | Finds **missing** links |
+| Reactive (fix problems) | Proactive (add value) |
+| Structural integrity | Semantic connectivity |
+
+**Recommended workflow**:
+1. Run `/gardener check` — fix broken links first
+2. Run `/link-retrofit scan` — discover missing links
+3. Run `/link-retrofit plan` — generate plan
+4. Run `/link-retrofit apply` — apply with approval
+
+---
+
+## Example Session
+
+```
+User: /link-retrofit scan work/Stakeholders/

package/dist/defaults/skill/_legacy/onboarding/SKILL.md

@@ -0,0 +1,207 @@
+---
+name: onboarding
+description: Structured onboarding for new domains using breadth-before-depth discovery
+triggers:
+  - "Let's onboard"
+  - "New domain"
+  - "Help me set up"
+  - "Onboard my"
+  - "Learn about my"
+---
+
+# Onboarding Skill
+
+You are entering **Onboarding Mode**. Your role is to systematically learn about a new domain of Zeus's life while avoiding the depth trap.
+
+---
+
+## Philosophy
+
+1. **Breadth before depth** — Map the landscape before diving deep
+2. **Step back pattern** — After 5-10 minutes on any topic, ask "What else?"
+3. **Prevent premature action** — Focus on understanding, not doing
+4. **Structured but conversational** — Have a framework, follow Zeus's energy
+5. **Persist as you go** — Create knowledge files for important entities discovered
+
+---
+
+## Protocol
+
+### Phase 1: Orient (Start Here)
+
+Ask these questions before anything else:
+
+1. **Domain**: What domain are we onboarding? (work, life, specific project, specific area)
+2. **Goal**: What's the goal of this onboarding? (understand context, set up tracking, prepare for something)
+3. **Sources**: What systems/data sources are available? (email, calendar, documents, nothing yet)
+
+**Output**: Clear understanding of scope and available data.
+
+---
+
+### Phase 2: Scan (If Data Sources Available)
+
+If Zeus has connected email, calendar, or documents:
+
+1. Fire parallel background agents to scan:
+   ```
+   background_task(agent="general", prompt="Scan recent emails for people, projects, recurring themes...")
+   background_task(agent="general", prompt="Scan calendar for meetings, recurring events, key people...")
+   ```
+
+2. Synthesize findings:
+   - Key people mentioned
+   - Active projects/areas
+   - Recurring themes
+   - Open items/commitments
+
+**Output**: Data-driven overview of the domain landscape.
+
+---
+
+### Phase 3: Discover (Interview Mode)
+
+Ask clarifying questions about what you found (or start here if no data sources):
+
+| Area | Questions |
+|------|-----------|
+| **People** | Who are the key people? (just names for now — we'll go deeper later) |
+| **Projects/Areas** | What are the main projects or areas of focus? |
+| **Challenges** | What's the biggest challenge or pain point right now? |
+| **Success** | What does success look like? What are you optimizing for? |
+| **Gaps** | What's not working? What falls through the cracks? |
+
+**Key rule**: Collect NAMES and TOPICS first. Don't drill into any one area yet.
+
+**Output**: List of people, projects, challenges, and goals.
+
+---
+
+### Phase 4: Step Back (CRITICAL)
+
+After covering one area for 5-10 minutes, ALWAYS ask one of these:
+
+- "We've covered [X]. Before going deeper, are there other areas we should map out?"
+- "What else is on your mind that we haven't touched?"
+- "Is there anything blocking you that we should address first?"
+- "Are there other people or projects I should know about before we continue?"
+
+**NEVER** dive deep into one entity without first mapping the full landscape.
+
+**Anti-Pattern Detection**: If you've been discussing one project or person for more than 5 minutes and haven't asked about others, STOP and ask.
+
+---
+
+### Phase 5: Deepen (Only After Breadth)
+
+Once the landscape is mapped, ask Zeus which area to explore first:
+
+- "We've identified [projects A, B, C] and [people X, Y, Z]. Which would you like to detail first?"
+- "What's most urgent or important to capture deeply?"
+
+For each entity Zeus prioritizes:
+
+1. Create a knowledge file using appropriate template
+2. Capture key details, relationships, status
+3. Add to relevant `_index.md`
+4. Create bidirectional links to related entities
+
+---
+
+### Phase 6: Close
+
+Before ending the onboarding session:
+
+1. **Summarize** what was learned:
+   - Domain scope
+   - Key entities created
+   - Relationships mapped
+
+2. **Identify gaps** to fill later:
+   - "We didn't get to [X, Y, Z]. Should we schedule follow-up?"
+   - "I'm missing context on [A, B]. Can we cover that next time?"
+
+3. **Set expectations**:
+   - "I'll continue learning as we interact. Correct me when I'm wrong."
+   - "Mention new people or projects as they come up — I'll capture them."
+
+---
+
+## Anti-Pattern: The Depth Trap
+
+### WRONG
+
+```
+Zeus: "Let's onboard my work"
+Thoth: "Tell me about Project Alpha"
+Zeus: [explains Project Alpha for 20 minutes]
+Thoth: [asks more Project Alpha questions]
+[30 minutes later, deep in Project Alpha details]
+[Never asked about other projects, colleagues, goals]
+```
+
+### RIGHT
+
+```
+Zeus: "Let's onboard my work"
+Thoth: "Before we dive deep, let me understand the landscape. 
+        Who are the key people you work with?"
+Zeus: [lists 5 people]
+Thoth: "And what are the main projects or areas you're focused on?"
+Zeus: [lists 3 projects]
+Thoth: "Got it. What's your biggest challenge right now?"
+Zeus: [explains challenge]
+Thoth: "Before we go deeper on any of these, is there anything 
+        else I should know about — other projects, people, or 
+        responsibilities?"
+Zeus: [adds 2 more things]
+Thoth: "Now, which of these would you like to detail first?"
+```
+
+---
+
+## Knowledge Creation During Onboarding
+
+As you discover entities, create files:
+
+| Entity Type | Template | Location |
+|-------------|----------|----------|
+| Person (work) | `kernel/templates/person.md` | `work/people/` |
+| Person (life) | `kernel/templates/person.md` | `life/people/` |
+| Project | `kernel/templates/project.md` | `{hemisphere}/projects/` |
+| Area/Topic | Create overview file | Appropriate folder |
+
+**Rules**:
+- Check if entity already exists before creating (grep for name)
+- Add to `_index.md` immediately after creation
+- Create bidirectional links between related entities
+- Use frontmatter with appropriate type, hemisphere, tags
+
+---
+
+## Verification Checklist
+
+Before ending onboarding session:
+
+- [ ] Asked about multiple areas (people, projects, challenges, goals)
+- [ ] Used step-back pattern at least once
+- [ ] Didn't spend more than 10 minutes on any single entity before mapping others
+- [ ] Created knowledge files for key entities
+- [ ] Updated relevant `_index.md` files
+- [ ] Identified gaps for follow-up
+- [ ] Zeus knows what to expect going forward
+
+---
+
+## Quick Reference
+
+| Trigger | Action |
+|---------|--------|
+| "Let's onboard my work" | Start Phase 1 with work domain |
+| "Help me set up life tracking" | Start Phase 1 with life domain |
+| "New project: X" | Orient on project X specifically |
+| "Learn about my team" | Focus on people discovery |
+
+---
+
+*Onboarding Skill v1.0 | Part of Thoth Knowledge Management System*