@jayjiang/byoao 1.1.2 → 2.0.0

package/src/assets/presets/common/SCHEMA.md.hbs

@@ -0,0 +1,57 @@
+# SCHEMA.md
+
+Knowledge taxonomy and conventions for [[{{KB_NAME}}]].
+
+## Knowledge Domains
+
+{{#if WIKI_DOMAIN}}
+{{WIKI_DOMAIN}}
+{{else}}
+Not yet defined. The Agent will populate this as it learns the domain.
+{{/if}}
+
+## Tag Taxonomy
+
+Tags follow these conventions:
+- 2-5 tags per page, alphabetically sorted
+- Tags should be singular (use `#project` not `#projects`)
+- New tags should be added here first before use
+
+### Current Tags
+
+No tags defined yet. The Agent will propose new tags as knowledge pages are created.
+
+## Domain Taxonomy
+
+No domains defined yet. The Agent will propose domains as knowledge pages are created.
+
+## Agent Page Conventions
+
+| Directory | Purpose |
+|-----------|---------|
+| `entities/` | Concrete, named things (people, organizations, products, systems) |
+| `concepts/` | Abstract ideas (methods, rules, decisions, processes) |
+| `comparisons/` | Side-by-side analyses of options |
+| `queries/` | User-question-driven answers worth keeping |
+
+## Frontmatter Schema
+
+See the /cook skill specification for the complete frontmatter schema. Key required fields:
+
+- `title` — concise one-line summary
+- `date` — primary temporal anchor (ISO 8601)
+- `created` — page creation date
+- `updated` — last content change date (bump on every edit)
+- `type` — one of: entity, concept, comparison, query
+- `tags` — 2-5 tags from this taxonomy, alphabetically sorted
+- `sources` — relative paths to contributing notes
+
+## Page Thresholds
+
+- Create a page when: entity/concept appears in 2+ notes OR is central subject of one note
+- Split a page when: it exceeds ~200 lines
+- Do NOT create pages for: passing mentions, minor details, out-of-domain topics
+
+## Custom Fields
+
+No custom fields defined yet. The Agent documents new fields here when first used.

package/src/assets/presets/common/Start Here.md.hbs

@@ -7,8 +7,8 @@ tags: [onboarding]
 
 # Welcome to {{KB_NAME}}
 
-Your personal knowledge base. Curate what matters, and let AI
-connect the dots into a knowledge graph.
+Your LLM-powered knowledge base. Write notes freely, and let AI
+compile them into structured, cross-referenced knowledge pages.
 
 ## Choose Your Path
 
@@ -25,58 +25,43 @@ you decide what belongs in your local knowledge base.
    and drop them into this vault folder.
 2. **Obsidian Web Clipper** — Install the browser extension to save
    any web page directly into your vault as a clean markdown note.
-3. **Write summaries** — You don't need full copies. Create a local
-   note that captures the key insights and link back to the source:
+3. **Write summaries** — Create a local note that captures key insights.
 
-```yaml
----
-title: "Migration Plan Q2"
-source: "https://confluence.example.com/pages/12345"
----
-```
-
-> The `source` property keeps the connection between your local note
-> and the cloud original. Add it whenever a note originates from an
-> external document.
-
-**Once you have a few notes → run `/weave`** (see below).
+**Once you have a few notes → run `/cook`** (see below).
 
 ### Path B: I already have local notes
 
-If you have existing markdown files — whether organized or scattered:
+If you have existing markdown files:
 
 1. **Drop them in** — Copy or move your files into this vault folder.
-   (Or if you ran `byoao init --from`, they're already here.)
-2. **Don't worry about structure** — Your files don't need frontmatter,
-   wikilinks, or any particular organization yet.
+2. **Don't worry about structure** — Your files don't need frontmatter
+   or any particular organization yet.
 
-**Run `/weave` now** — it will scan your notes, add frontmatter
-metadata (including dates from file timestamps), discover connections,
-and build your [[Glossary]] from frequently mentioned concepts.
+**Run `/cook` now** — it will scan your notes, identify entities and
+concepts, and compile them into structured knowledge pages.
 
 ### Path C: Starting fresh
 
 No existing notes? No problem.
 
 1. Press `Cmd+T` (Mac) or `Ctrl+T` (Windows) → choose "Daily Note".
-2. Write what's on your mind today. Don't worry about structure.
-3. After a few notes, run `/weave` to connect them.
+2. Write what's on your mind today.
+3. After a few notes, run `/cook` to compile them.
 
 ---
 
-## /weave — Where the Magic Happens
-
-Open your AI agent and type `/weave`. It will:
+## /cook — Where the Magic Happens
 
-- **Add frontmatter** — title, date, type, domain, tags
-- **Create wikilinks** — connect related notes automatically
-- **Build your Glossary** — extract key terms and concepts
-- **Suggest organization** — propose directory structure (with your approval)
+Open your AI agent and type `/cook`. It will:
 
-Watch: scattered files become a connected knowledge graph.
+- **Read your notes** — from anywhere in the vault
+- **Identify entities** — people, organizations, products, systems
+- **Identify concepts** — methods, rules, decisions, processes
+- **Create/update pages** — in `entities/`, `concepts/`, `comparisons/`, `queries/`
+- **Flag contradictions** — when notes disagree
+- **Report in plain language** — what changed, what needs your attention
 
-After weaving, press `Cmd+G` (Mac) or `Ctrl+G` (Windows) to see your
-knowledge visualized. Every node is a note, every line is a connection.
+After cooking, press `Cmd+G` to open Graph View and see the connections.
 
 ---
 
@@ -97,15 +82,17 @@ knowledge visualized. Every node is a note, every line is a connection.
 
 | Command | What it does |
 |---------|-------------|
-| `/weave` | Connect your notes into a knowledge graph |
-| `/organize` | Reorganize vault directories using enriched metadata |
+| `/cook` | Compile notes into structured knowledge pages |
+| `/health` | Check knowledge page health |
+| `/wiki` | Generate INDEX.base knowledge map |
+| `/organize` | Reorganize vault directories |
+| `/ask` | Open-ended Q&A against your knowledge |
 | `/trace` | Track how an idea evolved over time |
-| `/emerge` | Discover patterns you haven't noticed |
 | `/connect` | Bridge two seemingly unrelated topics |
 | `/ideas` | Generate actionable ideas from your vault |
 | `/challenge` | Pressure-test a belief against your own notes |
 | `/drift` | Compare intentions vs actions over time |
-| `/diagnose` | Check knowledge graph health |
+| `/diagnose` | Check overall vault health |
 
 {{#if HAS_MCP_SERVICES}}
 
@@ -122,11 +109,13 @@ These services authenticate via your browser. If a connection expires,
 tell the agent: "reconnect to {service name}".
 
 {{/if}}
+
 ---
 
 ## Key Files
 
-- **[[Glossary]]** — Domain terms and key concepts
+- **[[SCHEMA]]** — Tag taxonomy and knowledge conventions
+- **[[log]]** — Agent activity log
 - **AGENTS.md** — How AI agents navigate this vault
 
 ---

package/src/assets/presets/minimal/preset.json

@@ -1,9 +1,9 @@
 {
   "name": "minimal",
-  "displayName": "Personal Knowledge Base",
-  "description": "A minimal personal knowledge base — just Daily notes, templates, and Glossary. Add structure as you go.",
+  "displayName": "Minimal",
+  "description": "Core LLM Wiki with no extra MCP servers or role-specific directories",
   "directories": [],
-  "agentDescription": "Personal knowledge base. Notes are connected through wikilinks and frontmatter. Use /weave to discover and strengthen connections.",
+  "agentDescription": "LLM Wiki knowledge base. Use /cook to digest notes and external sources. Use /health to health-check.",
   "frontmatterExtras": {},
   "templates": [],
   "mcpServers": {},

package/src/assets/presets/pm-tpm/preset.json

@@ -1,9 +1,9 @@
 {
   "name": "pm-tpm",
   "displayName": "PM / TPM",
-  "description": "Project tracking, sprint cycles, stakeholder management, data analysis",
+  "description": "Adds Atlassian + BigQuery MCP servers, project directories, and PM templates on top of the core LLM Wiki",
   "directories": ["Projects", "Sprints"],
-  "agentDescription": "PM/TPM knowledge base",
+  "agentDescription": "LLM Wiki knowledge base with PM/TPM tooling. Use /cook to digest notes and external sources. Use /health to health-check. Atlassian and BigQuery are connected.",
   "frontmatterExtras": {
     "project": ["jira", "stakeholders", "priority"],
     "sprint": ["sprint-dates", "jira-board"]

package/src/skills/ask.md

@@ -1,11 +1,15 @@
 ---
 name: ask
-description: Open-ended Q&A against the knowledge base. Agent reads INDEX.base to locate relevant notes, synthesizes answers with citations. Use when the user asks questions about vault content like "what is X", "why did we decide", "explain Y", or wants to query their accumulated knowledge.
+description: >
+  Open-ended Q&A against the knowledge base. Agent reads INDEX.base for page discovery and
+  SCHEMA.md for tag taxonomy, navigates entities/, concepts/, comparisons/, and queries/,
+  synthesizes answers with citations. Use when the user asks questions about vault content like
+  "what is X", "why did we decide", "explain Y", or wants to query their accumulated knowledge.
 ---
 
 # /ask — Knowledge Q&A
 
-You are a knowledge assistant. Your job is to answer questions by navigating the vault's knowledge graph, reading relevant notes, and synthesizing evidence-based answers — always citing sources with wikilinks.
+You are a knowledge assistant. Your job is to answer questions by navigating the vault's knowledge graph, reading relevant pages, and synthesizing evidence-based answers — always citing sources with wikilinks.
 
 ## Prerequisites Check
 
@@ -15,7 +19,7 @@ You are a knowledge assistant. Your job is to answer questions by navigating the
 obsidian --version
 ```
 
-If this fails, STOP and display the Obsidian CLI availability message (see /weave for the full error text).
+If this fails, STOP and display the Obsidian CLI availability message (see /prep).
 
 ## Parameters
 
@@ -28,15 +32,17 @@ If this fails, STOP and display the Obsidian CLI availability message (see /weav
 
 Identify the key concepts, entities, and intent in the user's question.
 
-### Step 2: Locate Relevant Notes
+### Step 2: Locate Relevant Pages
 
-If `INDEX.base` exists, read it first to understand the vault structure:
+If `INDEX.base` exists, read it first for page discovery and the compiled knowledge map:
 
 ```bash
-obsidian read "INDEX"
+obsidian read file="INDEX.base"
 ```
 
-Then search for relevant notes:
+Read `SCHEMA.md` when you need the tag taxonomy, domain rules, or agent directory conventions.
+
+Then search for relevant pages:
 
 ```bash
 obsidian search "<key concept>"
@@ -44,25 +50,28 @@ obsidian search "<key concept>"
 
 Search for each key concept mentioned in the question. Combine results across concepts.
 
-### Step 3: Read Relevant Notes
+### Step 3: Read Relevant Pages
 
 For each promising result, read the full content:
 
 ```bash
-obsidian read "<note name>"
+obsidian read file="entities/some-page.md"
 ```
 
 Prioritize:
-- Notes with `note_type: permanent` (atomic concepts)
-- Highly linked notes (many backlinks)
-- Recent notes (last 30 days)
+- Agent pages in `entities/`, `concepts/`, `comparisons/`, `queries/`
+- Pages with matching tags or domain
+- Pages with `status: reviewed` (over `draft`)
+- Recent pages (higher `updated` date)
+
+Also read user source notes when the question requires original context.
 
 ### Step 4: Synthesize Answer
 
-Combine evidence from all relevant notes into a clear, structured answer:
+Combine evidence from all relevant pages into a clear, structured answer:
 
 - **Direct answer first** — address the question directly
-- **Supporting evidence** — cite specific notes with wikilinks and brief quotes
+- **Supporting evidence** — cite specific pages with wikilinks and brief quotes
 - **Context** — explain how the evidence connects
 - **Uncertainties** — flag gaps where the vault doesn't have enough information
 
@@ -77,9 +86,9 @@ Every claim must be backed by at least one vault note. Do not use general knowle
 
 ## Evidence
 
-- **[[Note A]]**: "<relevant quote>"
-- **[[Note B]]**: "<relevant quote>"
-- **[[Note C]]**: "<relevant quote>"
+- **[[Page A]]**: "<relevant quote>"
+- **[[Page B]]**: "<relevant quote>"
+- **[[Page C]]**: "<relevant quote>"
 
 ## Context
 
@@ -94,6 +103,7 @@ Every claim must be backed by at least one vault note. Do not use general knowle
 - Consider exploring: "..."
 - Run `/trace topic="X"` to see how this evolved
 - Run `/connect from="A" to="B"` to understand the relationship
+- If the vault lacks pages for key entities or concepts, run `/cook` to compile knowledge from source notes
 ```
 
 ### Step 6: Save (Optional)
@@ -107,21 +117,12 @@ If the user confirms, save the answer with frontmatter:
 ```yaml
 ---
 title: "Answer: <topic>"
-note_type: literature
-type: reference
-domain: <inferred>
 date: <today>
 tags: [qa, <topic>]
 ---
 ```
 
-Use `obsidian create` to save:
-
-```bash
-obsidian create name="Answer: <topic>" content="<frontmatter + content>" silent
-```
-
-Ask the user where they'd like it saved (root or a specific directory).
+Use `obsidian create` to save. Ask the user where they'd like it saved.
 
 ## Key Principles
 

package/src/skills/challenge.md

@@ -1,11 +1,14 @@
 ---
 name: challenge
-description: Pressure-test a belief, assumption, or decision using the vault's own history. Finds counter-evidence, contradictions, and blind spots. Use when the user says "challenge this", "am I wrong about", "test this assumption", "play devil's advocate", or wants to validate a decision against their own notes.
+description: >
+  Pressure-tests beliefs against vault evidence. Finds contradictions, position changes,
+  unstated assumptions, and weak points in arguments. Use when the user wants to question
+  a decision, test a hypothesis, or find flaws in their reasoning.
 ---
 
-# /challenge — Pressure-Test Your Thinking
+# /challenge — Pressure Test
 
-You are a constructive critic. Your job is to take a belief, assumption, or decision the user holds and rigorously test it against their own vault — finding counter-evidence, contradictions, unstated assumptions, and blind spots. You are not adversarial; you are helping the user think more clearly.
+You are a respectful adversary. Your job is to find the weak points in a belief, decision, or argument — not to be destructive, but to strengthen the user's thinking by exposing vulnerabilities they may have missed.
 
 ## Prerequisites Check
 
@@ -13,162 +16,117 @@ You are a constructive critic. Your job is to take a belief, assumption, or deci
 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.
+If this fails, STOP and display the Obsidian CLI availability message (see /prep).
 
 ## Parameters
 
-- **belief** (required): The belief, assumption, or decision to challenge. Can be a direct statement or a reference to a note.
-- **strength** (optional): "gentle" (look for nuances), "rigorous" (find every counter-argument). Default: "rigorous".
-- **output** (optional): Save the challenge analysis as a note.
+- **claim** (required): The belief, decision, or argument to challenge.
+- **scope** (optional): `all` (full vault) or a specific directory/page. Default: `all`.
 
 ## Process
 
-### Step 1: Articulate the Belief
-
-Parse the user's input and restate the belief clearly:
-
-> "The belief being tested: **{clear statement}**"
+### Step 1: Understand the Claim
 
-If the belief references a note, read it and extract the core claim:
+Clarify what exactly is being challenged:
+- What is the core assertion?
+- What assumptions does it rest on?
+- What would falsify it?
 
-```bash
-obsidian read "<note>"
-```
+If the claim is ambiguous, ask the user to clarify before proceeding.
 
 ### Step 2: Find Supporting Evidence
 
-First, be fair — find notes that support the belief:
-
 ```bash
-obsidian search "<key terms from belief>"
+obsidian search "<key terms from claim>"
 ```
 
-Read notes that discuss this topic. Document what supports the belief:
-- Which notes align with it?
-- What evidence was the belief originally based on?
-- How confident does the user seem in their notes?
-
-### Step 3: Find Counter-Evidence
-
-Now actively look for contradictions:
-
-**Direct contradictions** — Notes that explicitly state the opposite.
-
-**Changed positions** — Run a temporal analysis (like /trace):
-- Did the user ever hold a different view?
-- When did it change? What triggered it?
-- Was the change based on new evidence or assumption?
-
-**Unstated assumptions** — What does the belief take for granted?
-- "This assumes that {X} will remain true"
-- "This assumes that {person/team} agrees"
-- "This assumes the current constraints won't change"
-
-**Missing perspectives** — Whose viewpoint is absent?
-- "No notes consider the user/customer perspective"
-- "The cost analysis only covers engineering, not operations"
-
-**Survivorship bias** — Is the vault only tracking successes?
-- "Three similar initiatives are documented, all framed positively. Are there failed attempts that weren't documented?"
-
-### Step 4: Assess Confidence Level
+Read relevant notes and agent pages. Identify:
+- Notes that explicitly support the claim
+- Notes that provide indirect support (data, observations)
+- The strength of each piece of evidence
 
-Based on the evidence gathered, rate the belief:
+### Step 3: Find Contradicting Evidence
 
-| Level | Description |
-|-------|-------------|
-| **Strong** | Consistent support across notes, no meaningful counter-evidence, assumptions are reasonable |
-| **Moderate** | Good support but some counter-evidence exists, or key assumptions are untested |
-| **Weak** | Significant counter-evidence, contradictions over time, or critical unstated assumptions |
-| **Contradicted** | The vault's own history provides stronger evidence against the belief |
+This is the core of /challenge. Search for:
 
-### Step 5: Present the Challenge
+1. **Direct contradictions** — Notes that explicitly state the opposite
+   ```bash
+   obsidian search "not <term>" OR "instead of <term>" OR "changed from <term>"
+   ```
 
-```markdown
-# Challenge: {Belief Statement}
-
-**Confidence level**: {Strong / Moderate / Weak / Contradicted}
-
----
-
-## The Belief
-
-{Restated belief in the user's own words, citing the source note if applicable}
-
-## Supporting Evidence ({N} notes)
-
-- **[[Note]]**: "{quote supporting the belief}"
-- **[[Note]]**: "{quote}"
+2. **Implicit contradictions** — Notes that describe a situation incompatible with the claim
+   - Read pages with shared tags but different conclusions
+   - On related `entities/` and `concepts/` pages, check optional `contradictions` frontmatter (v2: YAML list of other agent page names documenting conflicting claims — see `/cook` Contradiction Handling)
 
-## Counter-Evidence ({N} notes)
+3. **Position changes over time** — Notes that show the user changed their mind
+   ```bash
+   obsidian search "actually" OR "turns out" OR "reconsidered" OR "reversed"
+   ```
 
-### Direct Contradictions
+4. **Weasel words** — Notes that express uncertainty about aspects the claim treats as certain
+   - "might", "probably", "not sure", "need to verify"
+   - These indicate the claim is stronger than the evidence supports
 
-- **[[Note]]** ({date}): "{quote that contradicts the belief}"
-  **Why this matters**: {explanation}
+### Step 4: Identify Unstated Assumptions
 
-### Position Changes Over Time
+For the claim to be true, what else must be true?
 
-- {date range}: You held view X (evidence: [[notes]])
-- {date}: Something shifted (trigger: [[note]])
-- {date range}: You now hold view Y
+- Technical assumptions (about systems, tools, constraints)
+- People assumptions (about availability, skills, priorities)
+- Temporal assumptions (about deadlines, sequencing, stability)
+- External assumptions (about market, users, dependencies)
 
-### Unstated Assumptions
+Check if the vault evidence supports each assumption.
 
-1. **{Assumption}**: {Why this might not hold}
-   Evidence: {what the vault says or doesn't say}
+### Step 5: Assess Evidence Strength
 
-2. **{Assumption}**: {Why this might not hold}
+Rate the overall case:
 
-### Missing Perspectives
+| Strength | Meaning |
+|----------|---------|
+| Strong | Multiple independent sources agree, no contradictions |
+| Moderate | Some support, minor gaps or contradictions |
+| Weak | Limited evidence, significant contradictions or gaps |
+| Unknown | Vault doesn't have enough information |
 
-- {Whose view is absent and why it matters}
+### Step 6: Present the Challenge
 
-## Verdict
-
-{2-3 paragraphs — fair assessment of how the belief holds up. Not a yes/no judgment but a nuanced analysis of where it's strong and where it's vulnerable.}
-
-## Questions to Sit With
+```markdown
+# Challenge: "{claim}"
 
-1. {A question the user should consider — not rhetorical, genuinely open}
-2. {Another question}
-3. {Another question}
+## The Claim
+{Restate the claim clearly}
 
-## Suggested Actions
+## What Rests On This
+{What assumptions does the claim depend on?}
+- {Assumption 1} — {supported / unsupported / contradicted}
+- {Assumption 2} — {supported / unsupported / contradicted}
 
-- {Concrete action if the belief needs revision}
-- {Action to gather missing evidence}
-- {Notes to re-read with fresh eyes}
-```
+## Supporting Evidence
+- [[Note A]]: "{quote}"
+- [[Note B]]: "{quote}"
 
-### Step 6: Save (Optional)
+## Challenging Evidence
+- ⚠ [[Note C]]: "{quote that contradicts or weakens the claim}"
+- ⚠ [[Note D]]: "{quote showing uncertainty or alternative view}"
 
-At the end of your challenge, ask:
+## Position Changes Over Time
+- {date}: [[Note E]] said X
+- {date}: [[Note F]] said Y (contradicts X)
 
-> "Would you like me to save this as a note?"
+## Weak Points
+1. **{Weak point}**: {why it's weak, which note shows it}
+2. **{Weak point}**: {why it's weak, which note shows it}
 
-If the user confirms, save with frontmatter:
+## Overall Assessment
+**Evidence strength**: {Strong / Moderate / Weak / Unknown}
 
-```yaml
----
-title: "Challenge: {Belief}"
-note_type: literature
-type: analysis
-date: <today>
-tags: [challenge, critical-thinking]
----
+{2-3 sentence summary: what the vault evidence suggests about this claim, what's uncertain, and what would strengthen or weaken the case further}
 ```
 
-Use `obsidian create` to save. Ask the user where they'd like it saved.
-
 ## Key Principles
 
-- **Fair, not adversarial**: Always present supporting evidence first. The goal is clear thinking, not winning an argument.
-- **Vault evidence only**: Challenge using the user's own notes, not general knowledge. "Research says X" is not valid here — "Your note from March says X" is.
-- **Name assumptions explicitly**: The most valuable output is often the unstated assumptions, not the direct contradictions.
-- **Questions over conclusions**: End with questions, not verdicts. The user decides what to do with the analysis.
-- **Respect the "strong" result**: If a belief holds up well, say so clearly. Not every challenge needs to find problems.
+- **Respectful opposition.** The goal is to strengthen thinking, not to tear it down. Frame challenges as "here's what to consider" not "you're wrong."
+- **Evidence only.** Every challenge must cite specific vault notes. Don't invent external counterarguments.
+- **Surface uncertainty.** If the vault shows doubt or hesitation about aspects the claim treats as certain, highlight this gap.
+- **Obsidian is first workbench.** All note operations go through Obsidian CLI.