@jayjiang/byoao 0.9.0 → 1.0.0-rc

package/dist/hooks/system-transform.js

@@ -62,6 +62,11 @@ function buildNavigationStrategy(vaultPath) {
         "| `references`| Related notes — follow for deeper context        |",
         "| `type`      | Note kind (meeting, idea, reference, daily, etc) |",
         "| `tags`      | Flexible categorization                          |",
+        "",
+        "### Vault Health",
+        "",
+        "If you notice broken wikilinks, orphan notes, or missing frontmatter while working,",
+        "suggest that the user run `/diagnose` to get a full vault health report.",
     ].join("\n");
 }
 /**

package/dist/hooks/system-transform.js.map

@@ -1 +1 @@
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package/dist/tools/init-vault.js

@@ -134,6 +134,12 @@ export const byoao_init_vault = tool({
         else {
             output += `\n\nOpen in Obsidian: "Open folder as vault" → select "${result.vaultPath}"`;
         }
+        if (result.initMode === "existing" || result.initMode === "obsidian-vault") {
+            output += `\n\n→ Next step: run /weave now — it will scan your existing notes, add frontmatter metadata (including dates), create wikilinks between related content, and build your Glossary from frequently mentioned concepts.`;
+        }
+        else {
+            output += `\n\n→ Next step: add a few notes, then run /weave to connect them into a knowledge graph. See "Start Here" in the vault for details.`;
+        }
         return output;
     },
 });

package/dist/tools/init-vault.js.map

@@ -1 +1 @@
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package/dist/vault/create.js

@@ -362,6 +362,7 @@ export async function createVault(config) {
         filesCreated: ctx.filesCreated,
         wikilinksCreated,
         directories: ctx.directories,
+        initMode,
         mcpResult,
         pluginsResult,
         providerResult,

package/dist/vault/create.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jayjiang/byoao",
-  "version": "0.9.0",
+  "version": "1.0.0-rc",
   "description": "Build Your Own AI OS — Obsidian + AI Agent",
   "type": "module",
   "engines": {

package/src/assets/obsidian-skills/byoao-conventions.md

@@ -16,9 +16,13 @@ Before creating any note:
 3. Identify the correct template — match your note type to a template below
 4. Verify the target directory — place the file according to its `type`
 
-## Creating Notes with Templates
+## Creating Notes
 
-ALWAYS use `obsidian create` when a matching template exists:
+You MUST use `obsidian create` to create notes in the vault — never use
+file write tools directly. Obsidian CLI ensures the file is tracked by
+Obsidian and templates are applied correctly.
+
+When a matching template exists:
 
 ```
 obsidian create name="Feature Name" template="Feature Doc" path="Projects/"
@@ -29,16 +33,11 @@ obsidian create name="Decision Title" template="Decision Record"
 obsidian create name="YYYY-MM-DD" template="Daily Note" path="Daily/"
 ```
 
-If no template matches, construct frontmatter manually:
+If no template matches, construct frontmatter manually. `date` MUST be
+today's actual date — never a placeholder, never omitted:
 
-```yaml
----
-title: "Note Title"
-type: reference
-status: draft
-date: YYYY-MM-DD
-tags: []
----
+```
+obsidian create name="Note Title" content="---\ntitle: \"Note Title\"\ntype: reference\nstatus: draft\ndate: 2026-04-02\ntags: []\n---\n\n# Note Title\n" silent
 ```
 
 ## Required Frontmatter

package/src/assets/obsidian-skills/vault-thinking.md

@@ -0,0 +1,40 @@
+---
+name: vault-thinking
+description: Guide for recommending BYOAO vault analysis commands to users. Use when the user is reflecting, brainstorming, stuck on an idea, asking about patterns, or could benefit from a vault-powered thinking workflow.
+---
+
+# Vault Thinking Guide
+
+This vault has BYOAO thinking commands available. Suggest them when they match the user's intent — don't wait for an exact keyword match.
+
+## Available Commands
+
+| Command | What it does | Suggest when |
+|---------|-------------|--------------|
+| `/weave` | Enrich notes with frontmatter, wikilinks, Glossary entries, hub notes | User imports new files, asks to organize, or vault has many unlinked notes |
+| `/trace topic` | Chronological timeline of how an idea evolved | User asks how something developed, wants history, or says "when did I start..." |
+| `/emerge` | Surface hidden patterns, clusters, contradictions across the vault | User asks "what am I missing", wants a big-picture review, or seems stuck |
+| `/connect A B` | Bridge two topics via the vault's link graph | User wonders if two areas are related, or wants cross-domain insight |
+| `/ideas` | Deep scan to generate actionable ideas from vault content | User asks "what should I work on", wants brainstorming, or needs next steps |
+| `/challenge topic` | Pressure-test a belief against the vault's own history | User is making a decision, says "am I wrong", or wants to validate an assumption |
+| `/drift` | Compare stated intentions vs actual behavior over 30-90 days | User asks about follow-through, wonders where time went, or reviews goals |
+| `/diagnose` | Vault health check — orphans, broken links, frontmatter gaps | User notices broken links, asks "what's wrong with my vault", or after heavy editing |
+## When to Proactively Suggest
+
+- User is **reflecting on a topic** → suggest `/trace` to see how their thinking evolved
+- User is **brainstorming or feels stuck** → suggest `/emerge` or `/ideas`
+- User is **making a decision** → suggest `/challenge` to pressure-test it
+- User is **reviewing goals or progress** → suggest `/drift`
+- User **imported new notes** or mentions disorganization → suggest `/weave`
+- User asks about **connections between topics** → suggest `/connect`
+- User mentions **broken links or vault messiness** → suggest `/diagnose`
+
+## How to Suggest
+
+Mention the command naturally in conversation. For example:
+
+- "You could run `/trace data-mesh` to see how that idea has evolved across your notes."
+- "If you want to pressure-test that assumption, `/challenge` can find counter-evidence in your vault."
+- "After importing those files, `/weave` can add frontmatter and link them to your existing notes."
+
+Do not run these commands automatically — they read many vault files and can take several minutes. Always let the user decide when to invoke them.

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

@@ -18,11 +18,14 @@
 
 | Field        | Purpose                                          |
 |-------------|--------------------------------------------------|
+| `title`     | Descriptive note title                           |
+| `date`      | YYYY-MM-DD — when the note was created           |
 | `domain`    | Knowledge area (e.g. analytics, infrastructure)  |
 | `type`      | Note kind (meeting, idea, reference, daily, etc) |
 | `references`| Related notes — follow for deeper context        |
 | `tags`      | Flexible categorization                          |
 | `status`    | draft / active / completed / archived            |
+| `source`    | (optional) URL to cloud origin — Confluence, Google Doc, etc. |
 
 {{{ROLE_SECTION}}}
 

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

@@ -7,33 +7,76 @@ tags: [onboarding]
 
 # Welcome to {{KB_NAME}}
 
-Your personal knowledge base. Write notes, import existing files,
-and let AI connect the dots.
+Your personal knowledge base. Curate what matters, and let AI
+connect the dots into a knowledge graph.
 
-## Get Started in 5 Minutes
+## Choose Your Path
 
-### 1. Import Your Existing Notes (optional)
+### Path A: My docs are in the cloud
 
-Already have files? Drop them into this vault folder, or use Obsidian
-Web Clipper to save web pages directly here.
+If your knowledge lives in Confluence, Google Docs, Notion, or other
+cloud services — you are the curator. BYOAO does not auto-import;
+you decide what belongs in your local knowledge base.
 
-### 2. Write Your First Daily Note
+**How to bring content in:**
 
-Press `Cmd+T` (Mac) or `Ctrl+T` (Windows) → choose "Daily Note".
-Write what's on your mind today. Don't worry about structure — just write.
+1. **Export as Markdown** — Confluence and Google Docs both support
+   exporting pages as `.md` files. Download the ones that matter
+   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. Run /weave
+```yaml
+---
+title: "Migration Plan Q2"
+source: "https://confluence.example.com/pages/12345"
+---
+```
 
-Open your AI agent and type `/weave`. It will scan your notes, discover
-connections, and add frontmatter + wikilinks.
+> The `source` property keeps the connection between your local note
+> and the cloud original. Add it whenever a note originates from an
+> external document.
 
-Watch: scattered files become a connected knowledge graph.
+**Once you have a few notes → run `/weave`** (see below).
+
+### Path B: I already have local notes
+
+If you have existing markdown files — whether organized or scattered:
+
+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.
+
+**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.
+
+### Path C: Starting fresh
 
-### 4. Explore the Graph
+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.
+
+---
+
+## /weave — Where the Magic Happens
+
+Open your AI agent and type `/weave`. It will:
+
+- **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)
+
+Watch: scattered files become a connected knowledge graph.
 
-Press `Cmd+G` (Mac) or `Ctrl+G` (Windows) to see your knowledge
-visualized. Every node is a note, every line is a connection
-that /weave discovered.
+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.
 
 ---
 
@@ -55,6 +98,7 @@ that /weave discovered.
 | Command | What it does |
 |---------|-------------|
 | `/weave` | Connect your notes into a knowledge graph |
+| `/organize` | Reorganize vault directories using enriched metadata |
 | `/trace` | Track how an idea evolved over time |
 | `/emerge` | Discover patterns you haven't noticed |
 | `/connect` | Bridge two seemingly unrelated topics |

package/src/skills/challenge.md

@@ -15,6 +15,10 @@ 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
 
 - **belief** (required): The belief, assumption, or decision to challenge. Can be a direct statement or a reference to a note.

package/src/skills/connect.md

@@ -15,6 +15,10 @@ 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
 
 - **from** (required): The first topic, concept, domain, or note.

package/src/skills/diagnose.md

@@ -58,7 +58,7 @@ For each issue category, suggest a concrete next action:
 
 ### Step 5: Update AGENT.md Timestamp
 
-After fixes are applied (with user consent), append or update a `Last Scanned` line at the bottom of AGENT.md:
+After fixes are applied, **ask the user** before updating AGENT.md. If confirmed, append or update a `Last Scanned` line at the bottom of AGENT.md:
 
 ```markdown
 ---

package/src/skills/drift.md

@@ -15,6 +15,10 @@ 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
 
 - **period** (optional): Time window to analyze. Default: "30d" (last 30 days). Accepts: "7d", "30d", "60d", "90d".
@@ -23,24 +27,39 @@ If this fails, STOP and display the Obsidian CLI availability message (see /weav
 
 ## Process
 
+### Date Range Resolution
+
+Calculate the cutoff date from the `period` parameter (e.g., "30d" = today minus 30 days). Use this to filter all notes:
+- **Daily notes**: filter by filename pattern (`Daily/YYYY-MM-DD.md`)
+- **Other notes**: filter by frontmatter `date` field
+- Notes without a date: include only if they are in an active project folder or have `status: active`
+
 ### Step 1: Collect Intentions
 
-Search for stated intentions, goals, and plans:
+Use a structured, layered approach to find stated intentions:
+
+**Layer 1 — Structured notes (most reliable):**
+```bash
+obsidian search "type: decision"
+obsidian search "type: plan"
+```
+Read sprint handoffs, project docs, and decision records within the period.
+
+**Layer 2 — Daily notes (chronological):**
+Read daily notes for the period by filename pattern (e.g., `Daily/2026-03-*.md`). Extract stated priorities, action items, and commitments.
 
+**Layer 3 — Keyword fallback (for vaults without structured frontmatter):**
+Only if Layers 1-2 produce fewer than 5 intentions:
 ```bash
 obsidian search "goal"
-obsidian search "plan"
-obsidian search "will do"
 obsidian search "next steps"
 obsidian search "TODO"
 obsidian search "priority"
 ```
 
 Also read:
-- Decision records — what was decided
-- Sprint/project plans — what was committed
-- Daily notes from the start of the period — stated priorities
-- Meeting notes — action items assigned
+- Meeting notes with action items assigned
+- Notes with tags like `#plan`, `#goal`, `#commitment`
 
 Extract a list of **stated intentions** with dates:
 - "{date}: Planned to {X}" (source: [[Note]])
@@ -88,6 +107,7 @@ Look for systemic patterns, not just individual misses:
 
 **Energy leaks** — Time going to undocumented work.
 > "Daily notes from weeks 3-5 rarely mention the stated priority. The gap suggests time is going somewhere not reflected in the vault."
+**Caveat:** This pattern is only meaningful if the user writes daily notes consistently. If daily notes are sparse or irregular, the absence of mentions is a documentation gap, not evidence of time spent elsewhere. Note this distinction in the report.
 
 **Goal abandonment** — Goals that silently disappeared.
 > "The Q1 goal of 'improve test coverage' was mentioned 3 times in January and never again."

package/src/skills/emerge.md

@@ -15,6 +15,10 @@ 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.
@@ -23,6 +27,10 @@ If this fails, STOP and display the Obsidian CLI availability message (see /weav
 
 ## 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:

package/src/skills/ideas.md

@@ -15,6 +15,10 @@ 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
 
 - **focus** (optional): Narrow ideas to a specific domain, project, or theme. Default: scan all domains.
@@ -23,6 +27,10 @@ If this fails, STOP and display the Obsidian CLI availability message (see /weav
 
 ## 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
 
 ```bash
@@ -70,6 +78,12 @@ Generate ideas across these categories:
 **Challenge ideas** — Question an assumption the vault takes for granted.
 > "Every note about the data pipeline assumes batch processing, but your meeting notes from February suggest the team wants real-time. Is batch still the right choice?"
 
+**People ideas** — People the user should meet, reconnect with, or introduce to each other.
+> "[[Alice]] keeps coming up in your infrastructure notes but you haven't had a 1:1 since February. Worth reconnecting."
+
+**Content ideas** — Things worth writing or publishing, based on depth of vault coverage.
+> "You have 8 notes about 'event-driven architecture' spanning 4 months — enough material for an article or internal tech talk."
+
 ### Step 5: Validate Each Idea
 
 For each idea, verify:
@@ -114,6 +128,14 @@ Generated from {N} notes across {M} domains.
 
 {Brief paragraph on themes across the ideas — are they pointing in the same direction?}
 
+## Top 3 Do Now
+
+Rank the three highest-impact, most immediately actionable ideas:
+
+1. **{Idea title}** — {one-sentence reason this is high-priority}
+2. **{Idea title}** — {reason}
+3. **{Idea title}** — {reason}
+
 ## Suggested Follow-ups
 
 - Run `/trace topic="X"` to explore Idea 1 further

package/src/skills/organize.md

@@ -0,0 +1,207 @@
+---
+name: organize
+description: Reorganize vault directory structure using Obsidian CLI's move command, which safely updates all backlinks. Analyzes enriched frontmatter (type, domain) to propose a logical folder layout. Use when the user says "organize my vault", "reorganize files", "clean up folders", "restructure", or after running /weave on a messy vault.
+---
+
+# /organize — Vault Directory Reorganization
+
+You are a vault organizer. Your job is to analyze the current directory structure, propose a logical reorganization based on enriched frontmatter metadata, and execute moves safely using Obsidian CLI — which automatically updates all backlinks and wikilinks.
+
+## Prerequisites Check
+
+**Before doing anything else:**
+
+1. 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
+```
+
+2. Check that files have frontmatter (specifically `type`). Run:
+
+```bash
+obsidian properties sort=count counts
+```
+
+If `type` property has very low coverage (< 30% of notes), STOP and suggest:
+
+```
+Most files lack a `type` property — /organize needs frontmatter to
+decide where files belong. Run /weave first to enrich your notes,
+then come back to /organize.
+```
+
+## Parameters
+
+- **scope** (optional): `all` (default) or a specific directory path to reorganize
+- **dry-run** (optional): If set, show proposed changes without executing
+- **aggressive** (optional): Also suggest consolidating existing directory structures (e.g., merge year-based sprint folders into `Sprints/`)
+
+## File Exclusion Rules
+
+Never move or suggest moving:
+
+| Pattern | Reason |
+|---------|--------|
+| `AGENT.md` | BYOAO-managed root file |
+| `Start Here.md` | BYOAO onboarding file |
+| `Knowledge/Glossary.md` | BYOAO Glossary |
+| `Knowledge/templates/*` | Template files |
+| `.obsidian/`, `.git/`, `.byoao/` | System directories |
+| `.opencode/`, `.cursor/`, `.claude/` | Tool config directories |
+| `.env`, `credentials.*`, `*.key` | Sensitive files |
+
+## Process
+
+### Step 1: Analyze Current Structure
+
+Build a complete picture of the vault:
+
+```bash
+obsidian list
+```
+
+Then read frontmatter for every file to build a map of `path → {type, domain, project, tags}`. Use batch reading:
+
+```bash
+obsidian read "<note name>"
+```
+
+Categorize every file into one of:
+- **Has type** — can be auto-organized based on the mapping table
+- **No type but in coherent directory** — already organized, leave in place
+- **No type and in root/flat dir** — suggest running `/weave` first
+
+### Step 2: Build Reorganization Map
+
+For each file with a `type` property, determine if it should move based on this mapping:
+
+| `type` | Target Directory | Notes |
+|--------|-----------------|-------|
+| `daily` | `Daily/` | |
+| `meeting` | Project folder if `project` field exists, else `Meetings/` | Group by project when possible |
+| `feature` | `Projects/<project>/` | Use `project` frontmatter field |
+| `project` | `Projects/` | Top-level project notes |
+| `sprint-handoff` | `Sprints/` | |
+| `reference` | `Knowledge/` | General reference material |
+| `person` | `People/` | |
+| `investigation` | Project folder if `project` field exists, else `Knowledge/` | |
+| `idea` | `Knowledge/` | |
+| `decision` | Project folder if `project` field exists, else `Knowledge/` | |
+
+**Smart rules — when NOT to move:**
+
+1. **Already in the right place** — if a `type: meeting` file is already in `Meetings/` or inside a project folder, skip it
+2. **Part of a coherent group** — if a file sits in `2025 Sprint/Sprint22/JIRA ticket/` alongside related files, the entire group is already organized even if the parent folder name doesn't match BYOAO conventions. Do NOT break up coherent groups
+3. **Deep nesting** — if a file is 3+ levels deep in a project-specific directory, it's likely intentionally placed. Leave it unless the user explicitly asks to flatten
+4. **Name collisions** — if moving a file would create a name collision in the target directory, flag it and skip
+
+**When `aggressive` mode is enabled**, also suggest structural consolidation:
+- Multiple year/sprint directories (e.g., `2025 Sprint/`, `2026 Sprint/`) → merge under `Sprints/2025/`, `Sprints/2026/`
+- Scattered documentation directories → consolidate under `Knowledge/`
+- This is a larger operation — always present as a separate approval step
+
+### Step 3: Present Plan
+
+Group proposed moves by category and show a clear summary:
+
+```
+/organize analysis complete.
+
+## Files to move (23 of 504)
+
+### Root files → proper directories
+  HANDOVER-2026-03-04.md → Knowledge/Handovers/HANDOVER-2026-03-04.md
+  HANDOVER-2026-03-02.md → Knowledge/Handovers/HANDOVER-2026-03-02.md
+  BigQuery_Syntax_Guide.md → Knowledge/BigQuery_Syntax_Guide.md
+
+### Meeting notes → Meetings/
+  standup-2026-03-15.md → Meetings/standup-2026-03-15.md
+
+### Reference docs → Knowledge/
+  API_Overview.md → Knowledge/API_Overview.md
+
+## New directories to create
+  Knowledge/Handovers/
+  Meetings/
+
+## Files staying in place: 481
+  (Already in coherent directory structures)
+
+## Files without `type` (cannot auto-organize): 12
+  Run /weave on these first, then re-run /organize.
+
+Options:
+  1. Approve all moves
+  2. Review one-by-one
+  3. Skip — make no changes
+```
+
+Wait for user response before proceeding.
+
+### Step 4: Execute Moves
+
+For each approved move, use `obsidian move`:
+
+```bash
+obsidian move file="HANDOVER-2026-03-04" to="Knowledge/Handovers/"
+```
+
+**Execution rules:**
+
+- Create target directories first if they don't exist:
+  ```bash
+  mkdir -p "<vault path>/<target directory>"
+  ```
+- Execute moves one at a time and verify each succeeds
+- If a move fails (name collision, file locked, etc.), log the error and continue with remaining moves
+- Report progress every 10 moves: "Moved 10/23 files..."
+
+**Why `obsidian move` instead of `mv`:**
+
+`obsidian move` tells Obsidian to perform the move internally. Obsidian automatically updates **all wikilinks and backlinks** across the entire vault that reference the moved file. Using file system `mv` would leave broken links.
+
+### Step 5: Verify
+
+After all moves complete:
+
+1. Get the updated file list:
+   ```bash
+   obsidian list
+   ```
+
+2. Check for broken links:
+   ```bash
+   byoao_graph_health
+   ```
+
+3. Report results:
+
+```
+/organize complete:
+  - Moved: 23 files
+  - Skipped: 0 (errors)
+  - New directories created: 2
+  - Broken links after moves: 0
+  - Files still without `type`: 12 (run /weave to fix)
+```
+
+If any broken links are found, report them and suggest fixes.
+
+## Important Guidelines
+
+- **Conservative by default**: Only suggest moves where the benefit is clear. A file that's "good enough" where it is should stay
+- **Never break coherent groups**: If files are organized together in a project directory, don't scatter them even if their `type` would suggest different target directories
+- **User approval is mandatory**: Never move files without explicit confirmation
+- **`obsidian move` only**: Never use file system `mv`, `cp`, or rename commands for vault files — only `obsidian move` and `obsidian rename` preserve link integrity
+- **Idempotent**: Running /organize twice should not propose moves for files that were already correctly placed in the first run
+- **Reversible**: If the user wants to undo, they can run `/organize` again with manual adjustments, or restore from git history

package/src/skills/trace.md

@@ -15,6 +15,10 @@ 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
 
 - **topic** (required): The idea, concept, person, project, or term to trace.
@@ -23,6 +27,10 @@ If this fails, STOP and display the Obsidian CLI availability message (see /weav
 
 ## Process
 
+### Sampling Strategy
+
+If a 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: Find All Mentions
 
 Search for the topic across the vault using multiple strategies:

package/src/skills/weave.md

@@ -1,6 +1,6 @@
 ---
 name: weave
-description: Scan vault notes, enrich with frontmatter + wikilinks, maintain the Glossary, create hub notes — building a connected knowledge graph. Use when the user says "connect my notes", "add links", "enrich", "organize my vault", "run weave", or after importing new files into the vault.
+description: Scan vault notes, enrich with frontmatter + wikilinks, maintain the Glossary, create hub notes — building a connected knowledge graph. Use when the user says "connect my notes", "add links", "enrich", "run weave", or after importing new files into the vault.
 ---
 
 # /weave — Connect Your Notes
@@ -47,8 +47,6 @@ When scanning files, skip:
 | `AGENT.md` | BYOAO-managed file |
 | `Knowledge/templates/` | Template files — not user content |
 
-Also respect `.byoaoignore` if present (same format as `.gitignore`).
-
 Report skipped non-markdown files at the end: "Skipped N non-markdown files".
 
 ## Process
@@ -111,16 +109,37 @@ If the file has no frontmatter, or has incomplete frontmatter, propose additions
 ---
 title: "<inferred from content or filename>"
 type: "<inferred: meeting, idea, reference, daily, project, person, etc>"
-date: <if identifiable from content>
+date: YYYY-MM-DD
 domain: "<knowledge area: analytics, infrastructure, design, etc>"
 references:
   - "[[Related Note]]"
   - "[[Glossary]]"
 tags: [<relevant tags>]
 status: <draft | active | completed | archived>
+source: "<URL if this note originates from a cloud document>"
 ---
 ```
 
+**Date resolution (mandatory — never leave empty):**
+
+1. Extract from content — explicit dates in the text, meeting dates, file name patterns (e.g. `2026-03-27-meeting.md`)
+2. If no date in content, get the file creation time:
+   ```bash
+   stat -f '%SB' -t '%Y-%m-%d' "<file path>"   # macOS
+   stat -c '%w' "<file path>"                    # Linux (birth time)
+   ```
+   If birth time is unavailable (`-` or empty), fall back to modification time:
+   ```bash
+   stat -f '%Sm' -t '%Y-%m-%d' "<file path>"    # macOS
+   stat -c '%y' "<file path>"                    # Linux
+   ```
+3. Never leave `date` empty in the proposed frontmatter.
+
+**Source field (optional):**
+
+- Add `source` only when the note clearly originates from a cloud document (e.g. contains Confluence export markers, Google Docs formatting, or a URL in the content pointing to the original).
+- If the file already has a `source` field, always preserve it.
+
 **Frontmatter preservation rules:**
 - **Never overwrite** existing fields
 - **Only add** missing fields
@@ -162,11 +181,21 @@ For each file with proposed changes:
 
 ### Step 6: Glossary Maintenance
 
-After scanning all files, analyze entity frequency:
+After scanning all files, analyze entity frequency and classify candidates:
+
+**High confidence (auto-suggest):** Entity appears in 5+ files AND has a clear,
+unambiguous definition (proper nouns, product names, acronyms, technical terms
+with standard meanings). Present as a batch for user review:
+- "'Kafka' mentioned in 8 notes — message streaming platform. Add to Glossary?"
 
-**New term suggestions:**
-- An entity appears in 3+ files but is not in the Glossary
-- Present each suggestion: "'Kafka' mentioned in 8 notes. Add to Glossary? (Y/n)"
+**Medium confidence (verify with user):** Entity appears in 3+ files but meaning
+is ambiguous or domain-specific. Ask the user to confirm the definition:
+- "'Migration' mentioned in 5 notes — what does this term mean in your context?"
+
+**Skip:** Common words, generic phrases, or terms that appear fewer than 3 times.
+Do not suggest these.
+
+- Always present Glossary additions as a batch for user review, not one-by-one
 - For confirmed terms, use `byoao_add_glossary_term` to add them
 
 **Auto-graduation suggestions:**
@@ -192,6 +221,7 @@ Identify entities that are frequently mentioned but have no corresponding note:
 ---
 title: "<Topic>"
 type: reference
+date: <today's date YYYY-MM-DD>
 domain: "<inferred domain>"
 references:
   - "[[note1]]"
@@ -210,7 +240,19 @@ status: active
 - [[note2]] — <brief context>
 ```
 
-### Step 8: Report
+### Step 8: Directory Organization (optional)
+
+If the vault has many files in flat or disorganized directories, suggest:
+
+"Your vault has files that could benefit from reorganization.
+Run `/organize` to see a proposed directory structure based on
+the frontmatter metadata we just added. It uses `obsidian move`
+to safely relocate files while automatically updating all links."
+
+Do NOT move files during /weave — directory reorganization is
+a separate step handled by `/organize`.
+
+### Step 9: Report
 
 After all changes are applied, provide a summary:
 

package/src/skills/explain.md

@@ -1,58 +0,0 @@
----
-name: explain
-description: Explain codebase systems and workflows in clear, non-jargon language, cached in the Obsidian vault. Use when the user asks "how does this system work", "explain the architecture", "what does this service do", or needs a plain-language explanation of any codebase or technical system.
----
-
-# /explain — System Explainer
-
-You are a codebase knowledge assistant for knowledge workers. Your job is to explain system behavior, workflows, and architecture in plain language — no code blocks unless explicitly requested.
-
-## Three-Layer Knowledge Strategy
-
-System knowledge comes from three sources, in priority order:
-
-```
-Layer 1: Baseline Overview    — Codebase overview per repo (high-level architecture)
-Layer 2: Live Code Access     — Local repo clone + file read/grep (detailed tracing)
-Layer 3: Knowledge Cache      — Obsidian Vault Systems/ (accumulated explanations)
-```
-
-### Layer 1: Baseline Overviews
-
-Engineers generate a codebase overview for each repo (e.g. via `opencode /init` or similar), containing architecture, key paths, conventions, and dependencies. These overviews are stored at:
-
-```
-.opencode/context/repos/
-  _index.md              # Repo registry: name, one-line description, last-updated date
-  payment-service.md     # Overview of payment-service repo
-  auth-service.md        # Overview of auth-service repo
-  api-gateway.md         # Overview of api-gateway repo
-```
-
-**Always load the relevant baseline overview first** before reading raw code.
-
-### Layer 2: Local Repo Clones
-
-For detailed questions, read the actual code from local clones at `~/repos/`. Use file read + grep + git log to trace specific workflows.
-
-### Layer 3: Obsidian Knowledge Cache
-
-Previously generated explanations are cached in `Systems/`. Reuse them when the question matches and the doc is still current.
-
-## Behavior
-
-1. **Parse the question** — identify the target system, service, or feature.
-2. **Load baseline overview** — read `.opencode/context/repos/{service}.md`.
-3. **Check Obsidian vault** — search `Systems/` for existing knowledge docs.
-4. **If more detail needed** — read the local repo clone using baseline as guide.
-5. **Staleness detection** — flag discrepancies between baseline and actual code.
-6. **Synthesize a clear explanation** with Mermaid diagrams where helpful.
-7. **Save to Obsidian vault** — create or update a doc in `Systems/`.
-
-## Output Style
-
-- Lead with **what the system does** (behavior), not how it's coded
-- Use workflow descriptions: "When X happens, the system does Y, then Z"
-- Include Mermaid diagrams for multi-step flows
-- No code blocks unless explicitly requested
-- Use `[[wikilinks]]` to connect related vault docs