@jayjiang/byoao 1.1.2 → 2.0.0

package/dist/vault/doctor.js

@@ -1,6 +1,12 @@
 import { fs } from "../lib/cjs-modules.js";
 import path from "node:path";
+import { stat } from "node:fs/promises";
 import { matter } from "../lib/cjs-modules.js";
+const LLM_WIKI_V2_AGENT_DIRS = ["entities", "concepts", "comparisons", "queries"];
+function isAgentWikiPage(relativePath) {
+    const top = relativePath.split(path.sep)[0];
+    return LLM_WIKI_V2_AGENT_DIRS.includes(top);
+}
 /** Recursively collect all .md files (excluding .obsidian) */
 async function collectMarkdownFiles(dir) {
     const results = [];
@@ -71,6 +77,18 @@ export async function getVaultDiagnosis(vaultPath) {
                 hasIssue = true;
             }
         }
+        const contra = data?.contradictions;
+        const contraList = Array.isArray(contra) &&
+            contra.some((x) => x != null && String(x).trim() !== "");
+        const contraStr = typeof contra === "string" && contra.trim() !== "";
+        if (contraList || contraStr) {
+            issues.push({
+                severity: "warning",
+                category: "contradiction",
+                file: relativePath,
+                message: "Note lists `contradictions` in frontmatter — review conflicting claims against linked agent pages",
+            });
+        }
         if (!hasIssue)
             healthyNotes++;
     }
@@ -98,6 +116,35 @@ export async function getVaultDiagnosis(vaultPath) {
             }
         }
     }
+    // LLM Wiki v2: agent directories and root index files
+    for (const dirName of LLM_WIKI_V2_AGENT_DIRS) {
+        const dirPath = path.join(vaultPath, dirName);
+        const exists = await fs.pathExists(dirPath);
+        const isDir = exists && (await stat(dirPath)).isDirectory();
+        if (!isDir) {
+            issues.push({
+                severity: "warning",
+                category: "agent-drift",
+                message: `LLM Wiki v2: expected agent directory \`${dirName}/\` at vault root`,
+            });
+        }
+    }
+    const schemaPath = path.join(vaultPath, "SCHEMA.md");
+    if (!(await fs.pathExists(schemaPath))) {
+        issues.push({
+            severity: "warning",
+            category: "agent-drift",
+            message: "LLM Wiki v2: missing SCHEMA.md at vault root",
+        });
+    }
+    const logMdPath = path.join(vaultPath, "log.md");
+    if (!(await fs.pathExists(logMdPath))) {
+        issues.push({
+            severity: "warning",
+            category: "agent-drift",
+            message: "LLM Wiki v2: missing log.md at vault root",
+        });
+    }
     // Check 4: Orphan notes (no incoming or outgoing wikilinks)
     const allLinksMap = new Map();
     const incomingLinks = new Set();
@@ -116,6 +163,8 @@ export async function getVaultDiagnosis(vaultPath) {
             continue;
         if (relativePath === "AGENT.md" || relativePath === "AGENTS.md")
             continue;
+        if (isAgentWikiPage(relativePath))
+            continue;
         const name = path.basename(filePath, ".md");
         const outgoing = allLinksMap.get(name) || new Set();
         const hasIncoming = incomingLinks.has(name);

package/dist/vault/doctor.js.map

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

@@ -1,7 +1,7 @@
 import { fs } from "../lib/cjs-modules.js";
 import path from "node:path";
 import { z } from "zod";
-const PKG_VERSION = "1.1.2";
+const PKG_VERSION = "2.0.0";
 // ── Schema ──────────────────────────────────────────────────────
 const InfrastructureSchema = z.object({
     skills: z.array(z.string()).default([]),

package/dist/vault/preset.js

@@ -2,13 +2,19 @@ import { fs } from "../lib/cjs-modules.js";
 import path from "node:path";
 import { PresetConfigSchema } from "../plugin-config.js";
 function getPresetsDir() {
+    // When running from dist/ (bundled): dist/assets/presets
+    const distAssets = path.resolve(import.meta.dirname, "assets", "presets");
+    // When running from dist/ via tsc only: ../assets/presets
     const srcPresets = path.resolve(import.meta.dirname, "..", "assets", "presets");
-    const distPresets = path.resolve(import.meta.dirname, "..", "..", "src", "assets", "presets");
+    // When running from src/ via tsx: ../../src/assets/presets
+    const devPresets = path.resolve(import.meta.dirname, "..", "..", "src", "assets", "presets");
+    if (fs.existsSync(distAssets))
+        return distAssets;
     if (fs.existsSync(srcPresets))
         return srcPresets;
-    if (fs.existsSync(distPresets))
-        return distPresets;
-    throw new Error(`Cannot find presets directory. Looked in:\n  ${srcPresets}\n  ${distPresets}`);
+    if (fs.existsSync(devPresets))
+        return devPresets;
+    throw new Error(`Cannot find presets directory. Looked in:\n  ${distAssets}\n  ${srcPresets}\n  ${devPresets}`);
 }
 export function listPresets() {
     const presetsDir = getPresetsDir();

package/dist/vault/preset.js.map

@@ -1 +1 @@
-{"version":3,"file":"preset.js","sourceRoot":"","sources":["../../src/vault/preset.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,EAAE,MAAM,uBAAuB,CAAC;AAC3C,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,kBAAkB,EAAqB,MAAM,qBAAqB,CAAC;AAE5E,SAAS,aAAa;IACpB,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;IAChF,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAC9B,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,SAAS,CAC5D,CAAC;IACF,IAAI,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;QAAE,OAAO,UAAU,CAAC;IACjD,IAAI,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC;QAAE,OAAO,WAAW,CAAC;IACnD,MAAM,IAAI,KAAK,CACb,gDAAgD,UAAU,OAAO,WAAW,EAAE,CAC/E,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,WAAW;IACzB,MAAM,UAAU,GAAG,aAAa,EAAE,CAAC;IACnC,MAAM,OAAO,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACpE,MAAM,OAAO,GAAiE,EAAE,CAAC;IAEjF,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,IAAI,KAAK,CAAC,IAAI,KAAK,QAAQ;YAAE,SAAS;QAC9D,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,IAAI,EAAE,aAAa,CAAC,CAAC;QACpE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;YAAE,SAAS;QACzC,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC;QACxC,MAAM,MAAM,GAAG,kBAAkB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAC7C,OAAO,CAAC,IAAI,CAAC;YACX,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,WAAW,EAAE,MAAM,CAAC,WAAW;YAC/B,WAAW,EAAE,MAAM,CAAC,WAAW;SAChC,CAAC,CAAC;IACL,CAAC;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,IAAY;IAIrC,MAAM,UAAU,GAAG,aAAa,EAAE,CAAC;IACnC,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC;IAC9C,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,aAAa,CAAC,CAAC;IAEvD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,MAAM,SAAS,GAAG,WAAW,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QACnD,MAAM,IAAI,KAAK,CACb,WAAW,IAAI,mCAAmC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACzE,CAAC;IACJ,CAAC;IAED,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC;IACxC,MAAM,MAAM,GAAG,kBAAkB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC7C,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;AAChC,CAAC;AAED,MAAM,UAAU,YAAY;IAC1B,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,EAAE,QAAQ,CAAC,CAAC;AAC9C,CAAC"}
+{"version":3,"file":"preset.js","sourceRoot":"","sources":["../../src/vault/preset.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,EAAE,MAAM,uBAAuB,CAAC;AAC3C,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,kBAAkB,EAAqB,MAAM,qBAAqB,CAAC;AAE5E,SAAS,aAAa;IACpB,yDAAyD;IACzD,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;IAC1E,0DAA0D;IAC1D,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;IAChF,2DAA2D;IAC3D,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;IAE7F,IAAI,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;QAAE,OAAO,UAAU,CAAC;IACjD,IAAI,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;QAAE,OAAO,UAAU,CAAC;IACjD,IAAI,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;QAAE,OAAO,UAAU,CAAC;IACjD,MAAM,IAAI,KAAK,CACb,gDAAgD,UAAU,OAAO,UAAU,OAAO,UAAU,EAAE,CAC/F,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,WAAW;IACzB,MAAM,UAAU,GAAG,aAAa,EAAE,CAAC;IACnC,MAAM,OAAO,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACpE,MAAM,OAAO,GAAiE,EAAE,CAAC;IAEjF,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,IAAI,KAAK,CAAC,IAAI,KAAK,QAAQ;YAAE,SAAS;QAC9D,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,IAAI,EAAE,aAAa,CAAC,CAAC;QACpE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;YAAE,SAAS;QACzC,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC;QACxC,MAAM,MAAM,GAAG,kBAAkB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAC7C,OAAO,CAAC,IAAI,CAAC;YACX,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,WAAW,EAAE,MAAM,CAAC,WAAW;YAC/B,WAAW,EAAE,MAAM,CAAC,WAAW;SAChC,CAAC,CAAC;IACL,CAAC;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,IAAY;IAIrC,MAAM,UAAU,GAAG,aAAa,EAAE,CAAC;IACnC,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC;IAC9C,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,aAAa,CAAC,CAAC;IAEvD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,MAAM,SAAS,GAAG,WAAW,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QACnD,MAAM,IAAI,KAAK,CACb,WAAW,IAAI,mCAAmC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACzE,CAAC;IACJ,CAAC;IAED,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC;IACxC,MAAM,MAAM,GAAG,kBAAkB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC7C,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;AAChC,CAAC;AAED,MAAM,UAAU,YAAY;IAC1B,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,EAAE,QAAQ,CAAC,CAAC;AAC9C,CAAC"}

package/dist/vault/self-update.js

@@ -1,6 +1,6 @@
 import { execSync } from "node:child_process";
 import { semver } from "../lib/cjs-modules.js";
-const PKG_VERSION = "1.1.2";
+const PKG_VERSION = "2.0.0";
 // ── Constants ───────────────────────────────────────────────────
 const PACKAGE_NAME = "@jayjiang/byoao";
 const REGISTRY_TIMEOUT_MS = 5_000;

package/dist/vault/status.js

@@ -50,6 +50,10 @@ export async function getVaultStatus(vaultPath) {
             directories: {},
             hasObsidianConfig: false,
             hasAgentMd: false,
+            agentPages: { entities: 0, concepts: 0, comparisons: 0, queries: 0 },
+            hasSchema: false,
+            hasLog: false,
+            hasIndexBase: false,
         };
     }
     const allFiles = await getAllMarkdownFiles(vaultPath);
@@ -86,6 +90,18 @@ export async function getVaultStatus(vaultPath) {
             directories[dir] = files.length;
         }
     }
+    const agentDirNames = ["entities", "concepts", "comparisons", "queries"];
+    const agentPages = {
+        entities: 0,
+        concepts: 0,
+        comparisons: 0,
+        queries: 0,
+    };
+    for (const name of agentDirNames) {
+        const dirPath = path.join(vaultPath, name);
+        const mdFiles = await getAllMarkdownFiles(dirPath);
+        agentPages[name] = mdFiles.length;
+    }
     return {
         exists: true,
         vaultPath,
@@ -96,6 +112,10 @@ export async function getVaultStatus(vaultPath) {
         hasObsidianConfig: await fs.pathExists(path.join(vaultPath, ".obsidian")),
         hasAgentMd: await fs.pathExists(path.join(vaultPath, "AGENTS.md")) ||
             await fs.pathExists(path.join(vaultPath, "AGENT.md")),
+        agentPages,
+        hasSchema: await fs.pathExists(path.join(vaultPath, "SCHEMA.md")),
+        hasLog: await fs.pathExists(path.join(vaultPath, "log.md")),
+        hasIndexBase: await fs.pathExists(path.join(vaultPath, "INDEX.base")),
     };
 }
 export function formatVaultStatus(status) {
@@ -115,6 +135,10 @@ export function formatVaultStatus(status) {
     lines.push("");
     lines.push(`Config: ${status.hasObsidianConfig ? "✓" : "✗"} .obsidian/`);
     lines.push(`Agent:  ${status.hasAgentMd ? "✓" : "✗"} AGENTS.md`);
+    lines.push("");
+    lines.push("LLM Wiki v2 (agent pages):");
+    lines.push(`  entities: ${status.agentPages.entities} · concepts: ${status.agentPages.concepts} · comparisons: ${status.agentPages.comparisons} · queries: ${status.agentPages.queries}`);
+    lines.push(`  SCHEMA.md: ${status.hasSchema ? "✓" : "✗"} · log.md: ${status.hasLog ? "✓" : "✗"} · INDEX.base: ${status.hasIndexBase ? "✓" : "✗"}`);
     if (status.brokenLinks.length > 0) {
         lines.push("");
         lines.push(`⚠️ Broken links (${status.brokenLinks.length}):`);

package/dist/vault/status.js.map

@@ -1 +1 @@
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+{"version":3,"file":"status.js","sourceRoot":"","sources":["../../src/vault/status.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,EAAE,MAAM,uBAAuB,CAAC;AAC3C,OAAO,IAAI,MAAM,WAAW,CAAC;AA0B7B,KAAK,UAAU,eAAe,CAAC,OAAe,EAAE,GAAG,GAAG,KAAK;IACzD,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC;QAAE,OAAO,CAAC,CAAC;IAC9C,MAAM,KAAK,GAAG,MAAM,EAAE,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;IACxC,OAAO,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC;AACrD,CAAC;AAED,KAAK,UAAU,mBAAmB,CAAC,OAAe;IAChD,MAAM,OAAO,GAAa,EAAE,CAAC;IAE7B,KAAK,UAAU,IAAI,CAAC,GAAW;QAC7B,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;YAAE,OAAO;QACxC,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;QAC/D,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;YAC5B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;YAC5C,IAAI,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;gBACxB,iCAAiC;gBACjC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;oBAChC,MAAM,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;iBAAM,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YACzB,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM,IAAI,CAAC,OAAO,CAAC,CAAC;IACpB,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,gBAAgB,CAAC,OAAe;IACvC,gEAAgE;IAChE,MAAM,QAAQ,GAAG,OAAO;SACrB,OAAO,CAAC,iBAAiB,EAAE,EAAE,CAAC,CAAG,qBAAqB;SACtD,OAAO,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC,CAAU,cAAc;IACnD,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,iCAAiC,CAAC,CAAC;IAClE,IAAI,CAAC,OAAO;QAAE,OAAO,EAAE,CAAC;IACxB,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,gCAAgC,EAAE,IAAI,CAAC,CAAC,CAAC;AAC/E,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,SAAiB;IACpD,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,UAAU,CAAC,SAAS,CAAC,CAAC;IAC9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAO;YACL,MAAM,EAAE,KAAK;YACb,SAAS;YACT,SAAS,EAAE,CAAC;YACZ,aAAa,EAAE,CAAC;YAChB,WAAW,EAAE,EAAE;YACf,WAAW,EAAE,EAAE;YACf,iBAAiB,EAAE,KAAK;YACxB,UAAU,EAAE,KAAK;YACjB,UAAU,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE;YACpE,SAAS,EAAE,KAAK;YAChB,MAAM,EAAE,KAAK;YACb,YAAY,EAAE,KAAK;SACpB,CAAC;IACJ,CAAC;IAED,MAAM,QAAQ,GAAG,MAAM,mBAAmB,CAAC,SAAS,CAAC,CAAC;IACtD,MAAM,SAAS,GAAG,IAAI,GAAG,CACvB,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,CAC7C,CAAC;IAEF,uCAAuC;IACvC,IAAI,aAAa,GAAG,CAAC,CAAC;IACtB,MAAM,cAAc,GAAG,IAAI,GAAG,EAAU,CAAC;IAEzC,KAAK,MAAM,IAAI,IAAI,QAAQ,EAAE,CAAC;QAC5B,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;QACjD,MAAM,KAAK,GAAG,gBAAgB,CAAC,OAAO,CAAC,CAAC;QACxC,aAAa,IAAI,KAAK,CAAC,MAAM,CAAC;QAE9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;gBACzB,cAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;YAC3B,CAAC;QACH,CAAC;IACH,CAAC;IAED,sBAAsB;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAC;IAC/C,MAAM,OAAO,GAAG;QACd,OAAO;QACP,UAAU;QACV,SAAS;QACT,WAAW;QACX,QAAQ;QACR,SAAS;QACT,SAAS;QACT,OAAO;KACR,CAAC;IACF,KAAK,MAAM,GAAG,IAAI,OAAO,EAAE,CAAC;QAC1B,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;QAC1C,IAAI,MAAM,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YACjC,MAAM,KAAK,GAAG,MAAM,mBAAmB,CAAC,OAAO,CAAC,CAAC;YACjD,WAAW,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC;QAClC,CAAC;IACH,CAAC;IAED,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,UAAU,EAAE,aAAa,EAAE,SAAS,CAAU,CAAC;IAClF,MAAM,UAAU,GAAG;QACjB,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,WAAW,EAAE,CAAC;QACd,OAAO,EAAE,CAAC;KACX,CAAC;IACF,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE,CAAC;QACjC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;QAC3C,MAAM,OAAO,GAAG,MAAM,mBAAmB,CAAC,OAAO,CAAC,CAAC;QACnD,UAAU,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,MAAM,CAAC;IACpC,CAAC;IAED,OAAO;QACL,MAAM,EAAE,IAAI;QACZ,SAAS;QACT,SAAS,EAAE,QAAQ,CAAC,MAAM;QAC1B,aAAa;QACb,WAAW,EAAE,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC;QACvC,WAAW;QACX,iBAAiB,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACzE,UAAU,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;YACtD,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,UAAU,CAAC,CAAC;QACjE,UAAU;QACV,SAAS,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACjE,MAAM,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QAC3D,YAAY,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC;KACtE,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,MAAmB;IACnD,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC;QACnB,OAAO,yBAAyB,MAAM,CAAC,SAAS,EAAE,CAAC;IACrD,CAAC;IAED,MAAM,KAAK,GAAa;QACtB,aAAa,MAAM,CAAC,SAAS,EAAE;QAC/B,aAAa,MAAM,CAAC,SAAS,EAAE;QAC/B,iBAAiB,MAAM,CAAC,aAAa,EAAE;QACvC,EAAE;QACF,sBAAsB;KACvB,CAAC;IAEF,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC;QAC9D,KAAK,CAAC,IAAI,CAAC,KAAK,GAAG,KAAK,KAAK,QAAQ,CAAC,CAAC;IACzC,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,WAAW,MAAM,CAAC,iBAAiB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,aAAa,CAAC,CAAC;IACzE,KAAK,CAAC,IAAI,CAAC,WAAW,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC;IACjE,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,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package/dist/vault/upgrade.js

@@ -2,13 +2,10 @@ import { fs } from "../lib/cjs-modules.js";
 import path from "node:path";
 import { readManifest, writeManifest, getPackageVersion, } from "./manifest.js";
 import { loadPreset, getCommonDir } from "./preset.js";
+import { renderTemplate } from "./template.js";
 import { detectVaultContext } from "./vault-detect.js";
 // ── Constants ───────────────────────────────────────────────────
-const OBSIDIAN_CONFIG_FILES = [
-    "core-plugins.json",
-    "daily-notes.json",
-    "templates.json",
-];
+const OBSIDIAN_CONFIG_FILES = ["core-plugins.json"];
 // ── Scanning ────────────────────────────────────────────────────
 /** Scan vault for installed infrastructure files. Returns relative paths. */
 export async function scanInstalledAssets(vaultPath) {
@@ -51,7 +48,7 @@ async function scanSkillDirs(vaultPath) {
     return results;
 }
 // ── Bootstrap ───────────────────────────────────────────────────
-const DEFAULT_PRESET = "pm-tpm";
+const DEFAULT_PRESET = "minimal";
 /** Bootstrap a manifest for vaults created before the manifest existed. */
 export async function bootstrapManifest(vaultPath, preset) {
     const installedFiles = await scanInstalledAssets(vaultPath);
@@ -98,26 +95,125 @@ export function buildUpgradePlan(vaultPath, manifest, packageAssets) {
         items,
     };
 }
+// ── v1→v2 migration ────────────────────────────────────────────
+const LLM_WIKI_AGENT_DIRS = ["entities", "concepts", "comparisons", "queries"];
+const LOG_MD_PLACEHOLDER = `# Agent Activity Log
+
+Entries are appended here during /cook operations.
+
+`;
+/** Create v2 wiki layout dirs and baseline files (idempotent). */
+async function migrateV1ToV2Infrastructure(vaultPath) {
+    for (const dir of LLM_WIKI_AGENT_DIRS) {
+        const dirPath = path.join(vaultPath, dir);
+        if (!(await fs.pathExists(dirPath))) {
+            await fs.ensureDir(dirPath);
+        }
+    }
+    const schemaPath = path.join(vaultPath, "SCHEMA.md");
+    if (!(await fs.pathExists(schemaPath))) {
+        const commonDir = getCommonDir();
+        const schemaTemplatePath = path.join(commonDir, "SCHEMA.md.hbs");
+        let content;
+        if (await fs.pathExists(schemaTemplatePath)) {
+            const schemaTemplate = await fs.readFile(schemaTemplatePath, "utf-8");
+            content = renderTemplate(schemaTemplate, {
+                KB_NAME: path.basename(vaultPath),
+                WIKI_DOMAIN: "",
+            });
+        }
+        else {
+            content = `# SCHEMA
+
+This file describes the vault knowledge schema. Update it as your model evolves.
+
+`;
+        }
+        await fs.writeFile(schemaPath, content, "utf-8");
+    }
+    const logPath = path.join(vaultPath, "log.md");
+    if (!(await fs.pathExists(logPath))) {
+        await fs.writeFile(logPath, LOG_MD_PLACEHOLDER, "utf-8");
+    }
+}
+/**
+ * v1 infrastructure still on disk that must appear as deprecated in the plan
+ * (Knowledge/templates/*.md; legacy weave/emerge commands). Merged after
+ * resolvePackageAssets + buildUpgradePlan — see mergeForcedDeprecatedIntoPlan.
+ */
+async function collectV1DeprecatedInfrastructureItems(vaultPath) {
+    const items = [];
+    const templatesDir = path.join(vaultPath, "Knowledge", "templates");
+    if (await fs.pathExists(templatesDir)) {
+        const files = await fs.readdir(templatesDir);
+        for (const f of files) {
+            if (f.endsWith(".md")) {
+                items.push({
+                    file: `Knowledge/templates/${f}`,
+                    action: "deprecated",
+                    category: "templates",
+                });
+            }
+        }
+    }
+    for (const cmd of ["weave.md", "emerge.md"]) {
+        const rel = `.opencode/commands/${cmd}`;
+        if (await fs.pathExists(path.join(vaultPath, rel))) {
+            items.push({
+                file: rel,
+                action: "deprecated",
+                category: "commands",
+            });
+        }
+    }
+    return items;
+}
+/** Prefer forced deprecation over add/update for the same path (v1 removals). */
+function mergeForcedDeprecatedIntoPlan(items, forced) {
+    const forcedFiles = new Set(forced.map((i) => i.file));
+    const filtered = items.filter((i) => !(forcedFiles.has(i.file) && (i.action === "add" || i.action === "update")));
+    const byFile = new Map(filtered.map((i) => [i.file, i]));
+    for (const f of forced) {
+        byFile.set(f.file, f);
+    }
+    return [...byFile.values()];
+}
 // ── Asset Resolution ────────────────────────────────────────────
 function resolveAssetsDir() {
+    // When running from dist/ (bundled): dist/assets
+    const distAssets = path.resolve(import.meta.dirname, "assets");
+    // When running from dist/ via tsc only: ../assets
     const srcAssets = path.resolve(import.meta.dirname, "..", "assets");
-    const distAssets = path.resolve(import.meta.dirname, "..", "..", "src", "assets");
-    if (fs.existsSync(srcAssets))
-        return srcAssets;
+    // When running from src/ via tsx: ../../src/assets
+    const devAssets = path.resolve(import.meta.dirname, "..", "..", "src", "assets");
     if (fs.existsSync(distAssets))
         return distAssets;
-    return srcAssets;
+    if (fs.existsSync(srcAssets))
+        return srcAssets;
+    if (fs.existsSync(devAssets))
+        return devAssets;
+    return distAssets; // will fail downstream with a clear error
 }
 function resolveSkillsDir() {
+    // When running from dist/ (bundled): dist/assets/skills
+    const distSkills = path.resolve(import.meta.dirname, "assets", "skills");
+    // When running from dist/ via tsc only: ../skills
     const srcSkills = path.resolve(import.meta.dirname, "..", "skills");
-    const distSkills = path.resolve(import.meta.dirname, "..", "..", "src", "skills");
-    if (fs.existsSync(srcSkills))
-        return srcSkills;
+    // When running from src/ via tsx: ../../src/skills
+    const devSkills = path.resolve(import.meta.dirname, "..", "..", "src", "skills");
     if (fs.existsSync(distSkills))
         return distSkills;
-    return srcSkills;
+    if (fs.existsSync(srcSkills))
+        return srcSkills;
+    if (fs.existsSync(devSkills))
+        return devSkills;
+    return distSkills;
 }
-/** Resolve package assets for a given preset. */
+/**
+ * Resolve package assets for a given preset.
+ * Legacy v1 paths (Knowledge/templates/*.md, weave/emerge commands on disk) are
+ * folded into the upgrade plan's deprecated items by collectV1DeprecatedInfrastructureItems.
+ */
 function resolvePackageAssets(preset) {
     const assetsDir = resolveAssetsDir();
     const skillsDir = resolveSkillsDir();
@@ -228,10 +324,18 @@ export async function upgradeVault(vaultPath, options) {
     if (!dryRun && await fs.pathExists(legacyAgentMd) && !await fs.pathExists(newAgentsMd)) {
         await fs.rename(legacyAgentMd, newAgentsMd);
     }
+    // 3c. v1→v2 vault layout (agent dirs, SCHEMA.md, log.md)
+    if (!dryRun) {
+        await migrateV1ToV2Infrastructure(vaultPath);
+    }
     // 4. Resolve package assets and build plan
     const effectivePreset = preset ?? manifest.preset;
     const packageAssets = resolvePackageAssets(effectivePreset);
-    const plan = buildUpgradePlan(vaultPath, manifest, packageAssets);
+    let plan = buildUpgradePlan(vaultPath, manifest, packageAssets);
+    plan = {
+        ...plan,
+        items: mergeForcedDeprecatedIntoPlan(plan.items, await collectV1DeprecatedInfrastructureItems(vaultPath)),
+    };
     // 5. Execute plan (or dry run)
     const added = [];
     const updated = [];

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jayjiang/byoao",
-  "version": "1.1.2",
+  "version": "2.0.0",
   "description": "Build Your Own AI OS — Obsidian + AI Agent",
   "type": "module",
   "engines": {

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

@@ -11,8 +11,8 @@ You MUST follow these conventions when creating or modifying any note in this va
 
 Before creating any note:
 
-1. Read `AGENTS.md` — check the knowledge base structure and note types
-2. Identify the note type: `fleeting` (raw input), `literature` (processed reference), or `permanent` (atomic concept)
+1. Read `AGENTS.md` — check the knowledge base structure (user notes vs agent-maintained pages)
+2. Decide where the note belongs: **user notes** stay in their existing areas (e.g. `Projects/`, `Daily/`); **agent knowledge pages** live only under `entities/`, `concepts/`, `comparisons/`, or `queries/`
 3. Use `obsidian create` to create notes — never use file write tools directly
 
 ## Creating Notes
@@ -32,8 +32,7 @@ Every note MUST have these fields:
 | Field | Values |
 |-------|--------|
 | `title` | Descriptive title |
-| `note_type` | `fleeting`, `literature`, or `permanent` |
-| `type` | `meeting`, `idea`, `reference`, `daily`, `project`, `person`, etc. |
+| `type` | `meeting`, `idea`, `reference`, `daily`, `project`, `person`, `entity`, `concept`, `comparison`, `query`, etc. |
 | `date` | YYYY-MM-DD — today's date or extracted from content |
 | `tags` | Array of relevant tags |
 
@@ -44,7 +43,10 @@ Additional fields (optional):
 | `domain` | Knowledge area (e.g. ai-agents, product-strategy) |
 | `references` | Related notes as wikilinks: `[[Note Name]]` |
 | `status` | `draft`, `active`, `completed`, `archived` |
-| `source` | URL to cloud origin (Confluence, Google Docs, etc.) |
+| `updated` | YYYY-MM-DD — last substantive edit (common on agent pages) |
+| `contradictions` | Cross-links when conflicting claims need review (agent pages) |
+
+For material **fetched from a single public URL** (e.g. web clip), you may add `source_url` and `fetched` (date). Do not use a generic `source` field for cloud documents.
 
 ## Wikilink Rules
 
@@ -65,7 +67,8 @@ Rules:
 
 - Use Title Case or kebab-case for file names
 - No special characters, no leading/trailing spaces
-- Daily notes: `YYYY-MM-DD` format
+- Daily notes: `YYYY-MM-DD` format where applicable
+- Agent knowledge pages: one topic per file under `entities/`, `concepts/`, `comparisons/`, or `queries/` (see `AGENTS.md` and `/cook`)
 
 ## Post-Creation Verification
 

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

@@ -11,21 +11,22 @@ This vault has BYOAO thinking commands available. Suggest them when they match t
 
 | Command | What it does | Suggest when |
 |---------|-------------|--------------|
-| `/weave` | Enrich notes with frontmatter, wikilinks, suggest permanent concept notes | User imports new files, asks to organize, or vault has many unlinked notes |
+| `/cook` | Digest notes and sources into structured knowledge pages under `entities/`, `concepts/`, `comparisons/`, `queries/` | User imports new files, asks to organize raw notes, or wants the vault compiled into LLM Wiki pages |
+| `/health` | Check knowledge-page health (orphans, stale content, contradictions among agent pages) | User wants a big-picture review of compiled knowledge, asks what's broken or outdated, or after heavy `/cook` activity |
 | `/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 **brainstorming or feels stuck** → suggest `/ideas` or `/health` on compiled knowledge
 - 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 **imported new notes** or mentions disorganization → suggest `/cook`
 - User asks about **connections between topics** → suggest `/connect`
 - User mentions **broken links or vault messiness** → suggest `/diagnose`
 
@@ -35,6 +36,6 @@ 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."
+- "After importing those files, `/cook` can distill them into linked knowledge pages under entities and concepts."
 
 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/AGENTS.md.hbs

@@ -1,25 +1,29 @@
 # AI Agent Guide
 
-## 关于本知识库
-这是一个基于 Zettelkasten 理念构建的个人知识库。知识通过原子化的笔记和双向链接形成网络。你可以保留自己的目录组织习惯，笔记之间的关联由 Agent 通过 `/weave` 自动维护。
+## About This Knowledge Base
+This is an LLM Wiki knowledge base. Your notes are raw material — the Agent compiles them into structured knowledge pages via `/cook`. Both coexist in the same vault, connected through wikilinks.
 
-## 从哪里开始
-知识图谱：运行 `/wiki` 生成 `INDEX.base` 后，从这里探索知识库的结构。
+## Getting Started
+Run `/wiki` to generate `INDEX.base`, then explore the knowledge structure from there.
 
-## 笔记类型
-每条笔记通过 frontmatter 的 `note_type` 分为三类：
-- **fleeting** — 原始摄入，待处理
-- **literature** — 对某来源的整理笔记
-- **permanent** — 原子概念笔记
+## Note Types
+User notes: Your existing notes, kept in their original directories (Projects/, Daily/, etc.) — untouched.
+Agent pages: Knowledge pages maintained by the Agent, located in `entities/`, `concepts/`, `comparisons/`, `queries/`.
 
-## 操作规则
-**使用 Obsidian CLI 进行所有笔记操作**（`obsidian read`、`obsidian search`、`obsidian create` 等）。
-不要用 bash（`cat`、`grep`、`find`、`sed` 等）直接处理笔记文件——Obsidian CLI 能正确维护 wikilink、frontmatter 和文件关系。
+## Operating Rules
+**Use Obsidian CLI for all note operations** (`obsidian read`, `obsidian search`, `obsidian create`, etc.).
+Do not use bash (`cat`, `grep`, `find`, `sed`, etc.) to manipulate note files directly — Obsidian CLI correctly maintains wikilinks, frontmatter, and file relationships.
 
-## 可用能力
-- **/weave** — 编织新笔记：提取概念、建立 wikilink、生成 frontmatter
-- **/wiki** — 生成 INDEX.base 知识图谱索引
-- **/organize** — 按需重组目录结构
-- **/ask** — 对知识库进行开放式问答
-- **Thinking Tools** — /trace、/emerge、/connect、/ideas、/challenge、/drift
-- **/diagnose** — 检查知识库健康状态，查看哪些笔记需要编织
+## Available Skills
+- **/cook** — Digest notes and external sources, compile knowledge pages
+- **/health** — Check knowledge page health (orphans, stale content, contradictions)
+- **/prep** — Fix frontmatter and broken wikilinks
+- **/wiki** — Generate INDEX.base knowledge map
+- **/organize** — Reorganize directory structure as needed
+- **/ask** — Open-ended Q&A against the knowledge base
+- **Thinking Tools** — /trace, /connect, /ideas, /challenge, /drift
+- **/diagnose** — Check overall vault health
+
+{{#if ROLE_SECTION}}
+## {{ROLE_SECTION}}
+{{/if}}