@jayjiang/byoao 1.1.2 → 2.0.0

package/src/skills/wiki.md

@@ -1,227 +1,126 @@
 ---
 name: wiki
-description: Generate INDEX.base knowledge graph at vault root and update AGENTS.md with current stats. Use when the user says "generate index", "build wiki", "update INDEX", "create knowledge map", or wants a visual overview of their vault.
+description: >
+  Generate and maintain INDEX.base — the dynamic knowledge map for v2 agent pages (`type`:
+  entity | concept | comparison | query). Uses Obsidian Base queries to list agent-maintained
+  pages; SCHEMA.md defines tag taxonomy. Use when the user runs /wiki or wants to see the current
+  state of the knowledge base.
 ---
 
-# /wiki — Generate Knowledge Index
+# /wiki — Knowledge Map
 
-You are a knowledge cartographer. Your job is to generate an `INDEX.base` file at the vault root that serves as the knowledge graph entry point, and update `AGENTS.md` with current vault statistics.
+**Metaphor:** The menu board — shows what's been prepared and what's on offer.
 
-## Prerequisites Check
+## Purpose
 
-**Before doing anything else**, verify Obsidian CLI is available:
-
-```bash
-obsidian --version
-```
-
-If this fails, STOP and display:
-
-```
-Obsidian CLI is not available. Please ensure:
-1. Obsidian is running
-2. This vault is open in Obsidian
-3. CLI is enabled: Settings → General → Advanced → Command-line interface
-```
+Generate and maintain `INDEX.base`, the dynamic knowledge map that lists all agent-maintained pages grouped by v2 `type` (`entity`, `concept`, `comparison`, `query`). Unlike static index files, INDEX.base uses Obsidian Base queries to stay current automatically. Use `SCHEMA.md` for tag taxonomy when summarizing or grouping entries.
 
 ## Process
 
-### Step 1: Build Vault Map
-
-```bash
-obsidian list
-```
+### Step 1: Prerequisites Check
 
 ```bash
-obsidian properties sort=count counts
+obsidian --version
 ```
 
-This gives you the full list of notes and their frontmatter distribution.
+If this fails, STOP and display the Obsidian CLI availability message (see /prep).
 
-### Step 2: Read Existing INDEX.base (if any)
-
-If `INDEX.base` already exists, read it to understand the current structure:
+### Step 2: Read SCHEMA.md
 
 ```bash
-obsidian read "INDEX"
+obsidian read file="SCHEMA.md"
 ```
 
-### Step 3: Analyze Knowledge Structure
-
-Group notes by their `domain` frontmatter field. For notes without `domain`, infer it from content. Count:
-- Total notes
-- Notes by `domain` (topics)
-- Notes by `note_type` (fleeting, literature, permanent)
-- Most frequently referenced concepts
+Understand the current tag taxonomy, domain definitions, and page conventions.
 
-### Step 4: Generate INDEX.base
+### Step 3: Generate INDEX.base Content
 
-Create or overwrite `INDEX.base` at the vault root. Use Obsidian CLI to create the file:
+Query all agent-maintained pages by v2 frontmatter `type` (`entity`, `concept`, `comparison`, `query`) so each page is listed under the correct section:
 
 ```bash
-obsidian create name="INDEX" content="<YAML content>" silent overwrite
+obsidian properties type=entity
+obsidian properties type=concept
+obsidian properties type=comparison
+obsidian properties type=query
 ```
 
-The content should be valid YAML for an Obsidian Base:
-
-```yaml
-filters:
-  not:
-    - 'note_type == ""'
-formulas: {}
-properties:
-  note_type:
-    displayName: Type
-  domain:
-    displayName: Domain
-views:
-  - type: table
-    name: "All Notes"
-    groupBy:
-      property: domain
-      direction: ASC
-    order:
-      - file.name
-      - note_type
-      - domain
-      - tags
-      - date
-  - type: cards
-    name: "Gallery"
-    groupBy:
-      property: note_type
-      direction: ASC
-    order:
-      - file.name
-      - note_type
-      - domain
-      - date
-```
+For each type, compile entries with:
+- Page name (as wikilink)
+- Title from frontmatter
+- Brief summary (from content's first paragraph or definition section)
+- Tags and domain
 
-**IMPORTANT:** The YAML must be properly formatted. Use single quotes for formulas containing special characters. Ensure proper indentation (2 spaces).
+Format by section:
 
-### Step 5: Generate AGENTS.md
+```markdown
+# Knowledge Index
 
-Read the current `AGENTS.md` (if it exists):
+## Entities
+- [[feature-a]] — Response time monitoring feature (tags: monitoring, backend)
+- [[zhang-san]] — Senior engineer on Feature A team (tags: team, engineering)
 
-```bash
-obsidian read "AGENTS"
-```
+## Concepts
+- [[response-time-metrics]] — Why median replaced avg for trigger calculation (tags: metrics, decisions)
+- [[search-trigger-rules]] — Search trigger rule design principles (tags: search, configuration)
 
-Generate a complete `AGENTS.md` that serves as the agent's entry point for the vault. Use `obsidian create` with `overwrite`:
+## Comparisons
+- [[avg-vs-median-for-trigger]] — Side-by-side analysis of avg vs median as trigger metrics (tags: metrics, decisions)
 
-```bash
-obsidian create path="AGENTS.md" content="<content>" overwrite silent
+## Queries
+- [[why-did-we-choose-median]] — "Why did we choose median over avg?" — detailed answer (tags: metrics, history)
 ```
 
-The AGENTS.md must contain these sections:
+### Step 4: Check Obsidian Base Configuration
 
-**Header**
-```markdown
-# BYOAO — Build Your Own AI OS
+INDEX.base relies on Obsidian Base (saved search) configuration. Verify:
 
-This knowledge base contains **M topics** and **N indexed notes**.
-```
+1. The Base query covers all four agent directories
+2. The query filters by `type` frontmatter field
+3. Results are grouped by type
 
-**Usage**
-```markdown
-## Usage
+If the Base doesn't exist or is misconfigured, guide the user to set it up:
+- Open Obsidian → Bases → Create new base
+- Name it "Knowledge Index"
+- Query: `path:entities/ OR path:concepts/ OR path:comparisons/ OR path:queries/`
+- Group by: `type`
 
-- `/weave` — Scan notes, enrich with frontmatter and wikilinks, build the knowledge graph
-- `/wiki` — Regenerate the INDEX.base knowledge map
-- `/organize` — Suggest a directory structure based on frontmatter metadata
-```
+### Step 5: Present the Index
 
-**Current Stats**
-```markdown
-## Current Stats
-
-- Total notes: {total}
-- Indexed notes (have note_type): {indexed}
-- Topics (domain): {domain1}, {domain2}, ...
-- Pending notes (need weave): {pending}
-```
+Show the current INDEX.base content to the user:
 
-**Interacting with the Vault** — This is critical. The agent must always prefer Obsidian CLI:
 ```markdown
-## Working with this Vault
-
-When you need to interact with notes, always use Obsidian CLI first:
-
-| Task | Command |
-|------|---------|
-| Search notes | `obsidian search query="keyword"` |
-| Read a note | `obsidian read file="Note Name"` |
-| Create a new note | `obsidian create name="Note Title" content="# Content"` |
-| Create note in folder | `obsidian create path="Folder/Note.md" content="# Content"` |
-| Append to a note | `obsidian append file="Note" content="New content"` |
-| Add frontmatter | `obsidian prepend file="Note" content='---
-title: "Title"
-note_type: fleeting
-domain: Topic
-date: YYYY-MM-DD
-tags: [tag1]
----
+# Knowledge Index
 
-'` |
-| Rename/move a note | `obsidian move path="Old.md" to="NewFolder/New.md"` |
-| List backlinks | `obsidian backlinks file="Note"` |
-| Check links | `obsidian links file="Note"` |
-| List all files | `obsidian files ext=md` |
-| Check unresolved links | `obsidian unresolved total` |
-| Open random note | `obsidian random` |
+Generated on YYYY-MM-DD
 
-For multi-line content, use `\\n` for newlines in the `content=` parameter.
-```
+Total pages: N (X entities, Y concepts, Z comparisons, W queries)
 
-**Creating New Notes** — explicit guidance:
-```markdown
-## Creating New Notes
-
-When asked to write, research, or document something:
-
-1. **Search first** — `obsidian search query="topic"` to check if a relevant note already exists
-2. **Read existing notes** — `obsidian read file="Note"` to understand what's already captured
-3. **Create with frontmatter** — always include proper YAML frontmatter when creating:
-   ```
-   obsidian create name="New Note" content='---
-   title: "New Note"
-   note_type: fleeting
-   domain: YourDomain
-   date: YYYY-MM-DD
-   tags: [relevant-tags]
-   ---
-
-   # New Note
-
-   Content here...
-   '
-   ```
-4. **Link to existing notes** — use `[[wikilink]]` syntax to connect new notes to existing ones
-5. **Use `/weave` after bulk creation** — to enrich and connect the new notes to the graph
-```
+## By Domain
+- backend: N pages
+- frontend: M pages
+- infrastructure: K pages
 
-**Footer**
-```markdown
----
-*Generated by /wiki skill*
-```
-
-### Step 6: Report
+## Most Connected
+- [[page-name]] — N inbound links
+- [[page-name]] — M inbound links
 
+## Recently Updated
+- [[page-name]] — updated YYYY-MM-DD
+- [[page-name]] — updated YYYY-MM-DD
 ```
-Wiki index generated:
-- INDEX.base: created/updated at vault root
-- Notes indexed: N
-- Topics: M (by domain)
-- AGENTS.md: updated with new counts
-```
 
-Suggest the user open `INDEX.base` in Obsidian to view the knowledge graph in table or card view.
+### Step 6: Suggest Gaps
+
+Based on the index, identify knowledge gaps:
+- Entity mentioned in multiple concepts but no entity page exists
+- Concept referenced in entity pages but no concept page exists
+- Domains with very few pages (under-represented areas)
+- Tags used frequently but no corresponding concept page
 
-## Important Guidelines
+## Key Principles
 
-- **INDEX.base is a query, not static content** — it dynamically displays notes based on frontmatter. The file itself only contains the query configuration.
-- **Only index notes with `note_type`** — notes without this field are not yet processed by `/weave` and should not appear in the index.
-- **Preserve custom views** — if the user has added custom views to `INDEX.base`, merge new views rather than overwriting.
-- **Idempotent** — running `/wiki` multiple times should produce the same result without duplication.
+- **INDEX.base is dynamic.** The Obsidian Base query keeps it current — no manual regeneration needed on every cook cycle.
+- **Summary quality.** Each entry's one-line summary should be genuinely informative, not just the page title repeated.
+- **Navigation first.** INDEX.base exists to help humans find knowledge quickly. Structure it for scanning, not completeness.
+- **Obsidian is first workbench.** All note operations go through Obsidian CLI.
+- **Agent pages only.** INDEX.base covers only `entities/`, `concepts/`, `comparisons/`, `queries/` — not user notes.

package/dist/assets/presets/common/Glossary.md.hbs

@@ -1,16 +0,0 @@
----
-title: Glossary
-type: reference
-status: active
-date: {{date}}
-tags: [glossary, reference]
----
-
-# Glossary
-
-Domain terms and key concepts in this knowledge base.
-Maintained by /weave — run it to discover and add new terms.
-
-| Term | Definition | Domain |
-|------|-----------|--------|
-{{GLOSSARY_ENTRIES}}

package/dist/assets/presets/common/obsidian/daily-notes.json

@@ -1,5 +0,0 @@
-{
-  "folder": "Daily",
-  "format": "YYYY-MM-DD",
-  "template": "Knowledge/templates/Daily Note"
-}

package/dist/assets/presets/common/obsidian/templates.json

@@ -1,3 +0,0 @@
-{
-  "folder": "Knowledge/templates"
-}

package/dist/assets/presets/common/templates/Daily Note.md

@@ -1,19 +0,0 @@
----
-title: "{{date}}"
-type: daily
-status: active
-date: {{date}}
-tags: [daily]
----
-
-## Focus
-
--
-
-## Notes
-
--
-
-## Action Items
-
-- [ ]

package/dist/assets/presets/common/templates/Decision Record.md

@@ -1,32 +0,0 @@
----
-title: ""
-type: decision
-status: draft
-date: {{date}}
-decision: ""
-decided-by: []
-alternatives-considered: []
-tags: [decision]
----
-
-## Context
-
-What is the situation that requires a decision?
-
-## Decision
-
-What was decided.
-
-## Alternatives Considered
-
-| Option | Pros | Cons |
-|--------|------|------|
-|        |      |      |
-
-## Rationale
-
-Why this option was chosen over alternatives.
-
-## Consequences
-
-What changes as a result of this decision.

package/dist/assets/presets/common/templates/Investigation.md

@@ -1,34 +0,0 @@
----
-title: ""
-type: investigation
-status: draft
-date: {{date}}
-jira: ""
-hypothesis: ""
-conclusion: ""
-tags: [investigation, spike]
----
-
-## Question
-
-What are we trying to find out?
-
-## Hypothesis
-
-What we expect to find and why.
-
-## Method
-
-How we investigated (queries, tools, data sources).
-
-## Findings
-
--
-
-## Conclusion
-
-Summary of what we learned. Does it confirm or refute the hypothesis?
-
-## Next Steps
-
--

package/dist/assets/presets/common/templates/Meeting Notes.md

@@ -1,25 +0,0 @@
----
-title: ""
-type: meeting
-status: active
-date: {{date}}
-participants: []
-meeting-type: ""
-tags: [meeting]
----
-
-## Agenda
-
-1.
-
-## Notes
-
--
-
-## Decisions
-
--
-
-## Action Items
-
-- [ ] @person — task — due date

package/dist/assets/skills/emerge.md

@@ -1,168 +0,0 @@
----
-name: emerge
-description: Surface conclusions, patterns, and insights the vault implies but never explicitly states. Analyzes clusters, orphans, and cross-domain connections. Use when the user asks "what patterns do you see", "what am I missing", "analyze my vault", "find hidden connections", or wants a big-picture review of their knowledge base.
----
-
-# /emerge — Surface Hidden Patterns
-
-You are a pattern recognition analyst. Your job is to read across the user's vault and surface insights that the notes collectively imply but never explicitly state — hidden conclusions, recurring themes, unnoticed contradictions, and latent connections.
-
-## Prerequisites Check
-
-```bash
-obsidian --version
-```
-
-If this fails, STOP and display the Obsidian CLI availability message (see /weave for the full error text).
-
-## Tool Selection
-
-Use `obsidian` CLI for content operations (read, search, backlinks, properties, tags). Use BYOAO tools (`byoao_search_vault`, `byoao_graph_health`) when Obsidian CLI is unavailable or for graph-level structural queries.
-
-## Parameters
-
-- **scope** (optional): Limit analysis to a folder, domain, or tag. Default: entire vault.
-- **depth** (optional): "quick" (top-level scan) or "deep" (read every note in scope). Default: "quick".
-- **output** (optional): If set, save findings as a note at this path.
-
-## Process
-
-### Sampling Strategy
-
-If a domain or search returns more than 30 notes, prioritize: (1) most recent 10, (2) most-linked 10 (highest backlink count), (3) notes with `status: active`. Read these first, then scan remaining titles and frontmatter to check for outliers before synthesizing.
-
-### Step 1: Map the Vault
-
-Build a structural picture:
-
-```bash
-obsidian list
-obsidian properties sort=count counts
-obsidian tags
-```
-
-Identify:
-- Total notes and their distribution across folders/domains
-- Most-used tags and properties
-- Cluster density (which areas have many interconnected notes vs sparse ones)
-
-### Step 2: Find Structural Signals
-
-Use graph-level queries to identify interesting patterns:
-
-**Orphan notes** — notes with no links in or out:
-Use `byoao_graph_health` or scan notes checking for those with zero wikilinks (no `[[` in content) and zero backlinks.
-Orphans may contain ideas the user hasn't connected yet.
-
-**Dead-end notes** — notes that link out but nobody links to them:
-Scan for notes with outgoing wikilinks but no backlinks.
-
-**Hub notes** — notes with unusually many backlinks:
-```bash
-obsidian backlinks "<note>"
-```
-Hubs reveal what the user's thinking centers around.
-
-**Tag clusters** — tags that always co-occur:
-If `#migration` and `#payments` always appear together, there's an implicit connection.
-
-### Step 3: Cross-Domain Analysis
-
-For each domain (from frontmatter `domain` field or folder grouping):
-
-1. **Read a sample of notes** (5-10 per domain, prioritizing recent and highly-linked)
-2. **Extract key themes** — what topics recur within the domain?
-3. **Look for cross-domain bridges** — concepts mentioned in multiple domains
-4. **Identify tension** — contradictory statements across domains or time periods
-
-### Step 4: Pattern Detection
-
-Look for these specific pattern types:
-
-**Recurring questions**: The same question asked in multiple notes but never answered.
-> "You've asked 'what's our rollback strategy?' in 4 different meeting notes but no note contains an answer."
-
-**Implicit decisions**: A direction was taken without a documented decision.
-> "Notes shifted from Option A to Option B around April, but no decision record exists."
-
-**Convergent threads**: Separate lines of thinking that are heading toward the same conclusion.
-> "Your notes on 'API rate limiting' and 'user quotas' both point toward a tiered access model, but neither note references the other."
-
-**Forgotten threads**: Topics that received attention then went silent.
-> "'Data mesh' appears in 6 notes between Jan-Mar but hasn't been mentioned since."
-
-**Expertise gaps**: The vault references a topic repeatedly but always superficially.
-> "'Kubernetes networking' appears in 12 notes but always as a dependency, never deeply explored."
-
-**Contradictions**: Conflicting statements across notes.
-> "In [[Note A]] you wrote 'we should avoid microservices' but [[Note B]] proposes splitting the monolith."
-
-### Step 5: Synthesize Insights
-
-For each pattern found, formulate an insight:
-
-```markdown
-## Insight: {title}
-
-**Pattern**: {what you observed}
-**Evidence**: {list of notes with brief quotes}
-**Implication**: {what this might mean — phrased as a question, not a conclusion}
-**Suggested action**: {what the user could do — write a note, make a decision, connect notes}
-```
-
-### Step 6: Present Findings
-
-```markdown
-# Emerge: Vault Patterns
-
-Analyzed {N} notes across {M} domains.
-
-## Key Findings
-
-### 1. {Insight title}
-{Pattern, evidence, implication, action}
-
-### 2. {Insight title}
-...
-
-## Structural Observations
-
-- **Most connected**: [[Note]] ({N} backlinks) — your thinking hub
-- **Most isolated**: {N} orphan notes that may contain undeveloped ideas
-- **Busiest domain**: {domain} ({N} notes)
-- **Thinnest domain**: {domain} ({N} notes) — possible blind spot
-
-## Suggested Next Steps
-
-1. {Actionable suggestion — e.g. "Connect [[A]] and [[B]] — they discuss the same problem"}
-2. {Actionable suggestion — e.g. "Write a decision record for the implicit choice between X and Y"}
-3. {Actionable suggestion — e.g. "Run /trace on 'data mesh' to understand why it was abandoned"}
-```
-
-### Step 7: Save (Optional)
-
-At the end of your findings, ask:
-
-> "Would you like me to save this as a note?"
-
-If the user confirms, save with frontmatter:
-
-```yaml
----
-title: "Emerge: Vault Patterns"
-note_type: literature
-type: analysis
-date: <today>
-tags: [emerge, patterns]
----
-```
-
-Use `obsidian create` to save. Ask the user where they'd like it saved.
-
-## Key Principles
-
-- **Show, don't tell**: Always cite specific notes and quotes. Never claim a pattern exists without evidence.
-- **Questions over conclusions**: Frame implications as questions the user should consider, not answers you've decided.
-- **Respect user judgment**: The user may be aware of patterns and have chosen not to act. Present findings neutrally.
-- **Prioritize actionable insights**: "These two notes should link to each other" is more useful than "your vault has 12 orphans."
-- **Deep mode means thorough**: In "deep" mode, read every note in scope. In "quick" mode, use structural signals and sampling.