@jayjiang/byoao 1.1.2 → 2.0.0

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,qDAAqD;AACrD,sDAAsD;AACtD,kEAAkE;AAGlE,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAC7D,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAC7D,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAC;AAC/D,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAC;AAClE,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EAAE,GAAG,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAC;AAEpD,MAAM,WAAW,GAAW,KAAK,EAAE,GAAG,EAAE,EAAE;IACxC,MAAM,EAAE,MAAM,EAAE,GAAG,GAAG,CAAC;IAEvB,MAAM,KAAK,GAAwB;QACjC,gBAAgB;QAChB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,mBAAmB;QACnB,cAAc;KACf,CAAC;IAEF,8CAA8C;IAC9C,KAAK,MAAM,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;QAChD,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAC;QACzB,GAAG,CAAC,OAAO,GAAG,KAAK,EAAE,IAAa,EAAE,OAAgB,EAAE,EAAE;YACtD,IAAI,CAAC;gBACH,OAAO,MAAM,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;YACnC,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,MAAM,KAAK,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClE,KAAK,GAAG,CAAC,OAAO,EAAE,QAAQ,IAAI,EAAE,EAAE,KAAK,CAAC,OAAO,EAAE;oBAC/C,KAAK;oBACL,OAAO,EAAE,YAAY,CAAC,IAAI,CAAC;iBAC5B,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,GAAE,CAAC,CAAC,CAAC;gBACnB,MAAM,GAAG,CAAC;YACZ,CAAC;QACH,CAAC,CAAC;IACJ,CAAC;IAED,gDAAgD;IAChD,MAAM,WAAW,GAA+B,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE;QACtE,IAAI,CAAC;YACH,OAAO,MAAM,mBAAmB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;QAClD,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,KAAK,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC;YAClE,KAAK,GAAG,CAAC,OAAO,EAAE,uBAAuB,EAAE,KAAK,CAAC,OAAO,EAAE;gBACxD,KAAK;aACN,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,GAAE,CAAC,CAAC,CAAC;YACnB,MAAM,GAAG,CAAC;QACZ,CAAC;IACH,CAAC,CAAC;IAEF,OAAO;QACL,IAAI,EAAE,KAAK;QACX,oCAAoC,EAAE,WAAW;QACjD,KAAK,EAAE,KAAK,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE;YACzB,IAAI,CAAC;gBACH,IAAI,KAAK,CAAC,IAAI,KAAK,cAAc,EAAE,CAAC;oBAClC,MAAM,UAAU,GAAG,iBAAiB,EAAE,CAAC;oBACvC,IAAI,UAAU,EAAE,CAAC;wBACf,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC;4BACnB,IAAI,EAAE;gCACJ,KAAK,EAAE,OAAO;gCACd,OAAO,EAAE,UAAU;gCACnB,OAAO,EAAE,MAAM;gCACf,QAAQ,EAAE,IAAI;6BACf;yBACF,CAAC,CAAC;oBACL,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,MAAM,KAAK,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClE,KAAK,GAAG,CAAC,OAAO,EAAE,SAAS,KAAK,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,OAAO,EAAE;oBACtD,KAAK;iBACN,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,GAAE,CAAC,CAAC,CAAC;YACrB,CAAC;QACH,CAAC;KACF,CAAC;AACJ,CAAC,CAAC;AAEF,eAAe,WAAW,CAAC"}

package/dist/plugin-config.js

@@ -1,50 +1,24 @@
 import { z } from "zod";
-export const MemberSchema = z.object({
-    name: z.string(),
-    role: z.string().default(""),
-});
-export const ProjectSchema = z.object({
-    name: z.string(),
-    description: z.string().default(""),
-});
-export const GlossaryEntrySchema = z.object({
+export const TaxonomyEntrySchema = z.object({
     term: z.string(),
     definition: z.string(),
     domain: z.string().default(""),
+    tags: z.array(z.string()).default([]),
 });
 export const VaultConfigSchema = z.object({
     kbName: z.string().min(1),
     ownerName: z.string().default(""),
     vaultPath: z.string(),
-    members: z.array(MemberSchema).default([]),
-    projects: z.array(ProjectSchema).default([]),
-    glossaryEntries: z.array(GlossaryEntrySchema).default([]),
-    jiraHost: z.string().default(""),
-    jiraProject: z.string().default(""),
     preset: z.string().default("minimal"),
     provider: z.enum(["copilot", "gemini", "skip"]).default("skip"),
     /** GCP Project ID — used for BigQuery MCP env and Gemini provider config */
     gcpProjectId: z.string().default(""),
     /** MCP server names to skip (user deselected in init flow) */
     mcpSkip: z.array(z.string()).default([]),
-});
-export const AddMemberSchema = z.object({
-    vaultPath: z.string(),
-    name: z.string(),
-    role: z.string().default(""),
-    team: z.string().default(""),
-});
-export const AddProjectSchema = z.object({
-    vaultPath: z.string(),
-    name: z.string(),
-    description: z.string().default(""),
-    team: z.string().default(""),
-});
-export const AddGlossaryTermSchema = z.object({
-    vaultPath: z.string(),
-    term: z.string(),
-    definition: z.string(),
-    domain: z.string().default(""),
+    /** What domain this knowledge base covers (used in SCHEMA.md generation) */
+    wikiDomain: z.string().default(""),
+    /** Agent autonomy level: auto = agent applies changes, review = agent reports first */
+    compilationMode: z.enum(["auto", "review"]).default("review"),
 });
 export const VaultStatusSchema = z.object({
     vaultPath: z.string(),

package/dist/plugin-config.js.map

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

@@ -5,7 +5,7 @@ import { VaultConfigSchema } from "../plugin-config.js";
 import path from "node:path";
 import os from "node:os";
 export const byoao_init_vault = tool({
-    description: "Create a personal knowledge base in Obsidian. Creates directory structure, templates, glossary, agent routing file (AGENTS.md), and optional people/project notes with wikilinks. Checks that Obsidian is installed first.",
+    description: "Create an LLM Wiki knowledge base in Obsidian. Sets up agent directories (entities/, concepts/, comparisons/, queries/), SCHEMA.md, log.md, and AI routing (AGENTS.md). Your existing notes become raw material for /cook.",
     args: {
         kbName: tool.schema.string().describe("Knowledge base name (e.g. \"Jay's KB\")"),
         ownerName: tool.schema.string().optional().describe("Owner's name"),
@@ -13,42 +13,16 @@ export const byoao_init_vault = tool({
             .string()
             .optional()
             .describe("Where to create the vault. Defaults to ~/Documents/{kbName}"),
-        members: tool.schema
-            .array(tool.schema.object({
-            name: tool.schema.string().describe("Person's name"),
-            role: tool.schema.string().optional().describe("Person's role"),
-        }))
-            .optional()
-            .describe("People to create notes for"),
-        projects: tool.schema
-            .array(tool.schema.object({
-            name: tool.schema.string().describe("Project name"),
-            description: tool.schema.string().optional().describe("One-line description"),
-        }))
-            .optional()
-            .describe("Active projects to create project notes for"),
-        glossaryEntries: tool.schema
-            .array(tool.schema.object({
-            term: tool.schema.string().describe("Domain term"),
-            definition: tool.schema.string().describe("Brief definition"),
-        }))
-            .optional()
-            .describe("Domain terms to add to the glossary"),
-        jiraHost: tool.schema
-            .string()
-            .optional()
-            .describe("JIRA host (e.g. 'mycompany.atlassian.net')"),
-        jiraProject: tool.schema
+        preset: tool.schema
             .string()
             .optional()
-            .describe("JIRA project key (e.g. 'HDR')"),
-        preset: tool.schema
+            .describe("Work profile (default: 'minimal'). Use 'pm-tpm' for PM/TPM with Atlassian + BigQuery."),
+        wikiDomain: tool.schema
             .string()
             .optional()
-            .describe("Role preset (default: 'minimal'). Use 'pm-tpm' for project management."),
+            .describe("What domain this knowledge base covers (e.g. 'AI/ML research', 'product management')"),
     },
     async execute(args) {
-        // Check Obsidian first
         const obsidianStatus = checkObsidian();
         if (!obsidianStatus.installed) {
             return `${formatObsidianStatus(obsidianStatus)}\n\nPlease install Obsidian first, then try again.`;
@@ -59,12 +33,8 @@ export const byoao_init_vault = tool({
             kbName: args.kbName,
             ownerName: args.ownerName || "",
             vaultPath: resolvedPath,
-            members: args.members || [],
-            projects: args.projects || [],
-            glossaryEntries: args.glossaryEntries || [],
-            jiraHost: args.jiraHost || "",
-            jiraProject: args.jiraProject || "",
             preset: args.preset || "minimal",
+            wikiDomain: args.wikiDomain || "",
         });
         const result = await createVault(config);
         let output = `✓ Knowledge base created at: ${result.vaultPath}\n`;
@@ -135,10 +105,10 @@ export const byoao_init_vault = tool({
             output += `\n\nOpen in Obsidian: "Open folder as vault" → select "${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.`;
+            output += `\n\n→ Next step: run /cook now — it will scan your existing notes, identify entities and concepts, and compile them into structured knowledge pages.`;
         }
         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.`;
+            output += `\n\n→ Next step: add a few notes, then run /cook to compile them into knowledge pages. 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/tools/vault-doctor.js

@@ -1,7 +1,7 @@
 import { tool } from "@opencode-ai/plugin/tool";
 import { getVaultDiagnosis } from "../vault/doctor.js";
 export const byoao_vault_doctor = tool({
-    description: "Scan an Obsidian vault and produce a diagnostic report. Checks: missing frontmatter, missing type/tags, AGENTS.md drift, orphan notes, broken wikilinks.",
+    description: "Scan an Obsidian vault and produce a diagnostic report. Checks: missing frontmatter, missing type/tags, AGENTS.md drift, orphan notes (user notes only; agent pages under entities/, concepts/, comparisons/, queries/ are excluded), broken wikilinks, LLM Wiki v2 layout (agent directories, SCHEMA.md, log.md at vault root), and notes with contradictions frontmatter.",
     args: {
         vaultPath: tool.schema.string().describe("Absolute path to the Obsidian vault"),
     },

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

@@ -1 +1 @@
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+{"version":3,"file":"vault-doctor.js","sourceRoot":"","sources":["../../src/tools/vault-doctor.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,0BAA0B,CAAC;AAChD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAEvD,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC;IACrC,WAAW,EACT,6WAA6W;IAC/W,IAAI,EAAE;QACJ,SAAS,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAChF;IACD,KAAK,CAAC,OAAO,CAAC,IAAI;QAChB,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QAEvD,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,oBAAoB,MAAM,CAAC,OAAO,CAAC,UAAU,WAAW,MAAM,CAAC,OAAO,CAAC,UAAU,SAAS,CAAC,CAAC;QACvG,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAEf,oBAAoB;QACpB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAgC,CAAC;QAC3D,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;YAClC,MAAM,GAAG,GAAG,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC;YACjD,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAChB,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;QACtC,CAAC;QAED,KAAK,MAAM,CAAC,QAAQ,EAAE,cAAc,CAAC,IAAI,UAAU,EAAE,CAAC;YACpD,MAAM,IAAI,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;YAClE,KAAK,CAAC,IAAI,CAAC,GAAG,IAAI,IAAI,QAAQ,KAAK,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;YAC7D,KAAK,MAAM,KAAK,IAAI,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC;gBAChD,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAClD,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,OAAO,GAAG,IAAI,EAAE,CAAC,CAAC;YAC1C,CAAC;YACD,IAAI,cAAc,CAAC,MAAM,GAAG,EAAE,EAAE,CAAC;gBAC/B,KAAK,CAAC,IAAI,CAAC,aAAa,cAAc,CAAC,MAAM,GAAG,EAAE,OAAO,CAAC,CAAC;YAC7D,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,IAAI,MAAM,CAAC,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;QACtD,CAAC;QAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1B,CAAC;CACF,CAAC,CAAC"}

package/dist/tools/vault-status.js

@@ -2,7 +2,7 @@ import { tool } from "@opencode-ai/plugin/tool";
 import { getVaultStatus, formatVaultStatus } from "../vault/status.js";
 import { checkObsidian, formatObsidianStatus } from "../vault/obsidian-check.js";
 export const byoao_vault_status = tool({
-    description: "Check the health of an Obsidian vault — note count, wikilink count, broken links, directory breakdown, and Obsidian installation status.",
+    description: "Check the health of an Obsidian vault — note count, wikilink count, broken links, directory breakdown, Obsidian installation status, and LLM Wiki v2 signals: per-directory markdown counts under entities/, concepts/, comparisons/, queries/, plus presence of SCHEMA.md, log.md, and INDEX.base at the vault root.",
     args: {
         vaultPath: tool.schema.string().describe("Path to the Obsidian vault"),
     },

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

@@ -1 +1 @@
-{"version":3,"file":"vault-status.js","sourceRoot":"","sources":["../../src/tools/vault-status.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,0BAA0B,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AACvE,OAAO,EAAE,aAAa,EAAE,oBAAoB,EAAE,MAAM,4BAA4B,CAAC;AAEjF,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC;IACrC,WAAW,EACT,0IAA0I;IAC5I,IAAI,EAAE;QACJ,SAAS,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;KACvE;IACD,KAAK,CAAC,OAAO,CAAC,IAAI;QAChB,MAAM,cAAc,GAAG,aAAa,EAAE,CAAC;QACvC,MAAM,WAAW,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QAEzD,IAAI,MAAM,GAAG,iBAAiB,CAAC,WAAW,CAAC,CAAC;QAC5C,MAAM,IAAI,+BAA+B,CAAC;QAC1C,MAAM,IAAI,oBAAoB,CAAC,cAAc,CAAC,CAAC;QAE/C,OAAO,MAAM,CAAC;IAChB,CAAC;CACF,CAAC,CAAC"}
+{"version":3,"file":"vault-status.js","sourceRoot":"","sources":["../../src/tools/vault-status.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,0BAA0B,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AACvE,OAAO,EAAE,aAAa,EAAE,oBAAoB,EAAE,MAAM,4BAA4B,CAAC;AAEjF,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC;IACrC,WAAW,EACT,uTAAuT;IACzT,IAAI,EAAE;QACJ,SAAS,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;KACvE;IACD,KAAK,CAAC,OAAO,CAAC,IAAI;QAChB,MAAM,cAAc,GAAG,aAAa,EAAE,CAAC;QACvC,MAAM,WAAW,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QAEzD,IAAI,MAAM,GAAG,iBAAiB,CAAC,WAAW,CAAC,CAAC;QAC5C,MAAM,IAAI,+BAA+B,CAAC;QAC1C,MAAM,IAAI,oBAAoB,CAAC,cAAc,CAAC,CAAC;QAE/C,OAAO,MAAM,CAAC;IAChB,CAAC;CACF,CAAC,CAAC"}

package/dist/vault/__tests__/create.test.js

@@ -4,7 +4,6 @@ import path from "node:path";
 import os from "node:os";
 import { createVault, } from "../create.js";
 import { detectInitMode } from "../vault-detect.js";
-// Mock mcp.ts so we don't touch real OpenCode config
 vi.mock("../mcp.js", () => ({
     configureMcp: vi.fn().mockResolvedValue(null),
 }));
@@ -26,105 +25,54 @@ function makeConfig(overrides = {}) {
         kbName: "TestKB",
         ownerName: "",
         vaultPath: path.join(tmpDir, "vault"),
-        members: [],
-        projects: [],
-        glossaryEntries: [],
-        jiraHost: "",
-        jiraProject: "",
-        preset: "pm-tpm",
+        preset: "minimal",
         provider: "skip",
         gcpProjectId: "",
         mcpSkip: [],
+        wikiDomain: "",
+        compilationMode: "review",
         ...overrides,
     };
 }
 describe("createVault", () => {
-    it("creates no default directories (vault starts empty)", async () => {
+    it("creates LLM Wiki agent directories", async () => {
         const result = await createVault(makeConfig());
-        // No default directories — vault starts empty
-        expect(result.directories).not.toContain("Knowledge");
-        expect(result.directories).not.toContain("Daily");
-        expect(result.directories).not.toContain("Knowledge/templates");
+        const vp = result.vaultPath;
+        expect(await fs.pathExists(path.join(vp, "entities"))).toBe(true);
+        expect(await fs.pathExists(path.join(vp, "concepts"))).toBe(true);
+        expect(await fs.pathExists(path.join(vp, "comparisons"))).toBe(true);
+        expect(await fs.pathExists(path.join(vp, "queries"))).toBe(true);
+        expect(result.directories).toContain("entities");
+        expect(result.directories).toContain("concepts");
+    });
+    it("creates SCHEMA.md and log.md", async () => {
+        const result = await createVault(makeConfig());
+        const vp = result.vaultPath;
+        expect(await fs.pathExists(path.join(vp, "SCHEMA.md"))).toBe(true);
+        expect(await fs.pathExists(path.join(vp, "log.md"))).toBe(true);
     });
-    it("generates AGENTS.md (no CLAUDE.md)", async () => {
+    it("generates AGENTS.md", async () => {
         const result = await createVault(makeConfig());
         const vp = result.vaultPath;
         expect(await fs.pathExists(path.join(vp, "AGENTS.md"))).toBe(true);
-        expect(await fs.pathExists(path.join(vp, "CLAUDE.md"))).toBe(false);
-        const agentContent = await fs.readFile(path.join(vp, "AGENTS.md"), "utf-8");
-        // New AGENTS.md is minimal — check for Zettelkasten reference
-        expect(agentContent).toContain("Zettelkasten");
     });
-    it("generates Start Here.md (no Glossary)", async () => {
+    it("generates Start Here.md", async () => {
         const result = await createVault(makeConfig());
         const vp = result.vaultPath;
         expect(await fs.pathExists(path.join(vp, "Start Here.md"))).toBe(true);
-        // No Glossary.md created
-        expect(await fs.pathExists(path.join(vp, "Knowledge/Glossary.md"))).toBe(false);
         const startHere = await fs.readFile(path.join(vp, "Start Here.md"), "utf-8");
         expect(startHere).toContain("TestKB");
     });
-    it("creates people notes from members config", async () => {
-        const config = makeConfig({
-            members: [
-                { name: "Alice", role: "Engineer" },
-                { name: "Bob", role: "PM" },
-            ],
-        });
-        const result = await createVault(config);
-        const vp = result.vaultPath;
-        const alice = await fs.readFile(path.join(vp, "People/Alice.md"), "utf-8");
-        expect(alice).toContain('type: person');
-        expect(alice).toContain("Engineer");
-        expect(await fs.pathExists(path.join(vp, "People/Bob.md"))).toBe(true);
-    });
-    it("creates project notes from projects config", async () => {
-        const config = makeConfig({
-            projects: [{ name: "Widget", description: "Build a widget" }],
-        });
-        const result = await createVault(config);
+    it("does not create People/ or Knowledge/ directories", async () => {
+        const result = await createVault(makeConfig());
         const vp = result.vaultPath;
-        const widget = await fs.readFile(path.join(vp, "Projects/Widget.md"), "utf-8");
-        expect(widget).toContain("type: feature");
-        expect(widget).toContain("Build a widget");
+        expect(await fs.pathExists(path.join(vp, "People"))).toBe(false);
+        expect(await fs.pathExists(path.join(vp, "Knowledge"))).toBe(false);
     });
     it("returns correct filesCreated count", async () => {
-        const config = makeConfig({
-            members: [{ name: "Alice", role: "Eng" }],
-            projects: [{ name: "P1", description: "desc" }],
-        });
-        const result = await createVault(config);
-        // At minimum: obsidian configs + templates + glossary + start here + agent + claude + 1 person + 1 project + team index
-        expect(result.filesCreated).toBeGreaterThanOrEqual(9);
-    });
-    it("tracks wikilinks created for members and projects", async () => {
-        const config = makeConfig({
-            members: [{ name: "Alice", role: "Eng" }],
-            projects: [{ name: "P1", description: "d" }],
-        });
-        const result = await createVault(config);
-        // members wikilinks in AGENTS.md + team index, projects in AGENTS.md + team index
-        expect(result.wikilinksCreated).toBeGreaterThanOrEqual(4);
-    });
-    it("populates wikilinks in team index", async () => {
-        const config = makeConfig({
-            members: [
-                { name: "Alice", role: "Eng" },
-                { name: "Bob", role: "PM" },
-            ],
-        });
-        const result = await createVault(config);
-        const teamIndex = await fs.readFile(path.join(result.vaultPath, "People/TestKB Team.md"), "utf-8");
-        expect(teamIndex).toContain("[[Alice]]");
-        expect(teamIndex).toContain("[[Bob]]");
-    });
-    it("glossary entries are ignored (feature removed)", async () => {
-        const config = makeConfig({
-            glossaryEntries: [{ term: "API", definition: "Application interface", domain: "engineering" }],
-        });
-        const result = await createVault(config);
-        // Glossary is no longer created — entries are safely ignored
-        expect(await fs.pathExists(path.join(result.vaultPath, "Knowledge/Glossary.md"))).toBe(false);
+        const result = await createVault(makeConfig());
+        // At minimum: obsidian configs + Start Here + SCHEMA.md + log.md + AGENTS.md + agent dirs
+        expect(result.filesCreated).toBeGreaterThanOrEqual(6);
     });
     it("writes .byoao/manifest.json after vault creation", async () => {
         const result = await createVault(makeConfig());
@@ -133,75 +81,59 @@ describe("createVault", () => {
         expect(await fs.pathExists(manifestPath)).toBe(true);
         const manifest = await fs.readJson(manifestPath);
         expect(manifest.version).toBeDefined();
-        expect(manifest.preset).toBe("pm-tpm");
+        expect(manifest.preset).toBe("minimal");
         expect(manifest.infrastructure.skills.length).toBeGreaterThan(0);
         expect(manifest.infrastructure.commands.length).toBeGreaterThan(0);
-        expect(manifest.infrastructure.templates.length).toBeGreaterThan(0);
     });
-    it("minimal preset creates no default directories", async () => {
+    it("minimal preset creates only LLM Wiki core directories", async () => {
         const config = makeConfig({ preset: "minimal" });
         const result = await createVault(config);
-        // No default directories — vault starts empty
-        expect(result.directories).toHaveLength(0);
-        // Minimal preset should NOT create these
-        expect(result.directories).not.toContain("Inbox");
-        expect(result.directories).not.toContain("Systems");
-        expect(result.directories).not.toContain("Archive");
-    });
-    it("minimal preset without members skips team index", async () => {
-        const config = makeConfig({ preset: "minimal", members: [] });
-        const result = await createVault(config);
-        const vp = result.vaultPath;
-        expect(await fs.pathExists(path.join(vp, "People"))).toBe(false);
-        expect(await fs.pathExists(path.join(vp, "People/TestKB Team.md"))).toBe(false);
-    });
-    it("minimal preset with members creates People/ and team index", async () => {
-        const config = makeConfig({
-            preset: "minimal",
-            members: [{ name: "Jay", role: "Owner" }],
-        });
-        const result = await createVault(config);
-        const vp = result.vaultPath;
-        expect(await fs.pathExists(path.join(vp, "People/Jay.md"))).toBe(true);
-        expect(await fs.pathExists(path.join(vp, "People/TestKB Team.md"))).toBe(true);
-    });
-    it("pm-tpm preset includes Projects and Sprints directories", async () => {
+        expect(result.directories).toContain("entities");
+        expect(result.directories).toContain("concepts");
+        expect(result.directories).toContain("comparisons");
+        expect(result.directories).toContain("queries");
+        expect(result.directories).not.toContain("Projects");
+        expect(result.directories).not.toContain("Sprints");
+    });
+    it("pm-tpm preset includes Projects and Sprints on top of LLM Wiki core", async () => {
         const config = makeConfig({ preset: "pm-tpm" });
         const result = await createVault(config);
+        expect(result.directories).toContain("entities");
+        expect(result.directories).toContain("concepts");
         expect(result.directories).toContain("Projects");
         expect(result.directories).toContain("Sprints");
     });
     it("preserves existing .obsidian/ when initializing in an Obsidian vault", async () => {
         const vp = path.join(tmpDir, "vault");
-        // Pre-create an existing Obsidian vault with custom config
         await fs.ensureDir(path.join(vp, ".obsidian"));
         await fs.writeFile(path.join(vp, ".obsidian", "custom-theme.json"), '{"custom": true}');
         await fs.writeFile(path.join(vp, "existing-note.md"), "# My Note\n\nHello");
         const config = makeConfig({ preset: "minimal" });
         const result = await createVault(config);
-        // .obsidian/ should be untouched — custom file preserved, no BYOAO configs injected
         const customTheme = await fs.readFile(path.join(vp, ".obsidian", "custom-theme.json"), "utf-8");
         expect(customTheme).toContain('"custom": true');
-        // BYOAO files should still be created
         expect(await fs.pathExists(path.join(vp, "AGENTS.md"))).toBe(true);
-        // No Glossary in new design
         expect(await fs.pathExists(path.join(vp, "Start Here.md"))).toBe(true);
-        // Existing note should be untouched
+        expect(await fs.pathExists(path.join(vp, "SCHEMA.md"))).toBe(true);
         const existingNote = await fs.readFile(path.join(vp, "existing-note.md"), "utf-8");
         expect(existingNote).toContain("My Note");
     });
-    it("does not overwrite existing AGENT.md or Start Here.md", async () => {
+    it("does not overwrite existing Start Here.md", async () => {
         const vp = path.join(tmpDir, "vault");
         await fs.ensureDir(vp);
-        await fs.writeFile(path.join(vp, "AGENT.md"), "# Custom Agent Config");
         await fs.writeFile(path.join(vp, "Start Here.md"), "# My Custom Start");
         const config = makeConfig({ preset: "minimal" });
         await createVault(config);
-        const agentContent = await fs.readFile(path.join(vp, "AGENT.md"), "utf-8");
-        expect(agentContent).toBe("# Custom Agent Config");
         const startHere = await fs.readFile(path.join(vp, "Start Here.md"), "utf-8");
         expect(startHere).toBe("# My Custom Start");
     });
+    it("includes wikiDomain in SCHEMA.md when provided", async () => {
+        const config = makeConfig({ wikiDomain: "AI/ML research" });
+        const result = await createVault(config);
+        const vp = result.vaultPath;
+        const schema = await fs.readFile(path.join(vp, "SCHEMA.md"), "utf-8");
+        expect(schema).toContain("AI/ML research");
+    });
 });
 describe("detectInitMode", () => {
     it("returns 'fresh' for non-existent path", () => {

package/dist/vault/__tests__/create.test.js.map

@@ -1 +1 @@
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package/dist/vault/__tests__/doctor.test.js

@@ -25,12 +25,18 @@ function noteWithFrontmatter(fields, body = "") {
 }
 describe("getVaultDiagnosis", () => {
     it("reports zero issues for a clean vault", async () => {
+        await fs.ensureDir(path.join(tmpDir, "entities"));
+        await fs.ensureDir(path.join(tmpDir, "concepts"));
+        await fs.ensureDir(path.join(tmpDir, "comparisons"));
+        await fs.ensureDir(path.join(tmpDir, "queries"));
+        await writeNote("SCHEMA.md", noteWithFrontmatter({ type: "reference", tags: ["wiki"] }, "# Schema\n\nSee [[note]]\n"));
+        await writeNote("log.md", noteWithFrontmatter({ type: "reference", tags: ["wiki"] }, "# Log\n\nSee [[note]]\n"));
         await writeNote("note.md", noteWithFrontmatter({ type: "reference", tags: ["test"] }, "See [[other]]\n"));
         await writeNote("other.md", noteWithFrontmatter({ type: "reference", tags: ["test"] }, "Back to [[note]]\n"));
         const report = await getVaultDiagnosis(tmpDir);
         expect(report.issues).toHaveLength(0);
-        expect(report.summary.totalNotes).toBe(2);
-        expect(report.summary.healthyNotes).toBe(2);
+        expect(report.summary.totalNotes).toBe(4);
+        expect(report.summary.healthyNotes).toBe(4);
     });
     it("reports missing frontmatter", async () => {
         await writeNote("bare.md", "# No frontmatter\n\nJust text.");
@@ -68,6 +74,12 @@ describe("getVaultDiagnosis", () => {
         expect(brokenLinks[0].message).toContain("[[nonexistent]]");
     });
     it("reports AGENT.md drift", async () => {
+        await fs.ensureDir(path.join(tmpDir, "entities"));
+        await fs.ensureDir(path.join(tmpDir, "concepts"));
+        await fs.ensureDir(path.join(tmpDir, "comparisons"));
+        await fs.ensureDir(path.join(tmpDir, "queries"));
+        await writeNote("SCHEMA.md", noteWithFrontmatter({ type: "reference", tags: ["wiki"] }, "[[Alice]]"));
+        await writeNote("log.md", noteWithFrontmatter({ type: "reference", tags: ["wiki"] }, "[[Alice]]"));
         await writeNote("AGENT.md", "Team: [[Alice]] and [[Bob]]");
         await fs.ensureDir(path.join(tmpDir, "People"));
         await writeNote("People/Alice.md", noteWithFrontmatter({ type: "person", tags: ["person"] }));

package/dist/vault/__tests__/doctor.test.js.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.test.js","sourceRoot":"","sources":["../../../src/vault/__tests__/doctor.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAC;AACrE,OAAO,EAAE,MAAM,UAAU,CAAC;AAC1B,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAEjD,IAAI,MAAc,CAAC;AAEnB,UAAU,CAAC,KAAK,IAAI,EAAE;IACpB,MAAM,GAAG,MAAM,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,eAAe,CAAC,CAAC,CAAC;AACrE,CAAC,CAAC,CAAC;AAEH,SAAS,CAAC,KAAK,IAAI,EAAE;IACnB,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;AAC1B,CAAC,CAAC,CAAC;AAEH,SAAS,SAAS,CAAC,IAAY,EAAE,OAAe;IAC9C,OAAO,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE,OAAO,CAAC,CAAC;AACxD,CAAC;AAED,SAAS,mBAAmB,CAAC,MAA+B,EAAE,IAAI,GAAG,EAAE;IACrE,MAAM,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC;SAChC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;QACd,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;YAAE,OAAO,GAAG,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;QACvD,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;IACtB,CAAC,CAAC;SACD,IAAI,CAAC,IAAI,CAAC,CAAC;IACd,OAAO,QAAQ,IAAI,YAAY,IAAI,EAAE,CAAC;AACxC,CAAC;AAED,QAAQ,CAAC,mBAAmB,EAAE,GAAG,EAAE;IACjC,EAAE,CAAC,uCAAuC,EAAE,KAAK,IAAI,EAAE;QACrD,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAAC;QAClD,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAAC;QAClD,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC,CAAC;QACrD,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC,CAAC;QACjD,MAAM,SAAS,CACb,WAAW,EACX,mBAAmB,CACjB,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EACrC,4BAA4B,CAC7B,CACF,CAAC;QACF,MAAM,SAAS,CACb,QAAQ,EACR,mBAAmB,CACjB,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EACrC,yBAAyB,CAC1B,CACF,CAAC;QACF,MAAM,SAAS,CACb,SAAS,EACT,mBAAmB,CACjB,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EACrC,iBAAiB,CAClB,CACF,CAAC;QACF,MAAM,SAAS,CACb,UAAU,EACV,mBAAmB,CACjB,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EACrC,oBAAoB,CACrB,CACF,CAAC;QAEF,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC/C,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;QACtC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAC1C,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAC9C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,6BAA6B,EAAE,KAAK,IAAI,EAAE;QAC3C,MAAM,SAAS,CAAC,SAAS,EAAE,gCAAgC,CAAC,CAAC;QAE7D,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC/C,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,aAAa,CAAC,CAAC;QAC3E,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,CAAC;QAClD,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,SAAS,CAAC,qBAAqB,CAAC,CAAC;IAC/D,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,4BAA4B,EAAE,KAAK,IAAI,EAAE;QAC1C,MAAM,SAAS,CACb,YAAY,EACZ,mBAAmB,CAAC,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EAAE,SAAS,CAAC,CACnD,CAAC;QAEF,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC/C,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CACzC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAC,CACrC,CAAC;QACF,MAAM,CAAC,SAAS,CAAC,CAAC,WAAW,EAAE,CAAC;QAChC,MAAM,CAAC,SAAU,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;IAC9C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,4BAA4B,EAAE,KAAK,IAAI,EAAE;QAC1C,MAAM,SAAS,CACb,YAAY,EACZ,mBAAmB,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,SAAS,CAAC,CACtD,CAAC;QAEF,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC/C,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CACzC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAC,CACrC,CAAC;QACF,MAAM,CAAC,SAAS,CAAC,CAAC,WAAW,EAAE,CAAC;QAChC,MAAM,CAAC,SAAU,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAC3C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,sBAAsB,EAAE,KAAK,IAAI,EAAE;QACpC,MAAM,SAAS,CACb,WAAW,EACX,mBAAmB,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EAAE,WAAW,CAAC,CACxE,CAAC;QAEF,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC/C,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC;QAC1E,MAAM,CAAC,YAAY,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;QACrC,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;IACjD,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,0BAA0B,EAAE,KAAK,IAAI,EAAE;QACxC,MAAM,SAAS,CACb,WAAW,EACX,mBAAmB,CACjB,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE,EACrC,0BAA0B,CAC3B,CACF,CAAC;QAEF,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC/C,MAAM,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CACtC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,aAAa,CACpC,CAAC;QACF,MAAM,CAAC,WAAW,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;QACpC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,SAAS,CAAC,iBAAiB,CAAC,CAAC;IAC9D,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,wBAAwB,EAAE,KAAK,IAAI,EAAE;QACtC,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAAC;QAClD,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAAC;QAClD,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC,CAAC;QACrD,MAAM,EAAE,CAAC,SAAS,CAAC,I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package/dist/vault/__tests__/manifest.test.js

@@ -16,7 +16,7 @@ describe("writeManifest", () => {
             skills: [".opencode/skills/byoao-conventions/SKILL.md"],
             commands: [".opencode/commands/vault-doctor.md"],
             obsidianConfig: [".obsidian/core-plugins.json"],
-            templates: ["Knowledge/templates/Daily Note.md"],
+            templates: ["Knowledge/templates/Example.md"],
         };
         await writeManifest(tmpDir, "pm-tpm", installedFiles);
         const manifestPath = path.join(tmpDir, ".byoao", "manifest.json");
@@ -29,7 +29,7 @@ describe("writeManifest", () => {
         expect(manifest.infrastructure.skills).toEqual([".opencode/skills/byoao-conventions/SKILL.md"]);
         expect(manifest.infrastructure.commands).toEqual([".opencode/commands/vault-doctor.md"]);
         expect(manifest.infrastructure.obsidianConfig).toEqual([".obsidian/core-plugins.json"]);
-        expect(manifest.infrastructure.templates).toEqual(["Knowledge/templates/Daily Note.md"]);
+        expect(manifest.infrastructure.templates).toEqual(["Knowledge/templates/Example.md"]);
     });
     it("creates .byoao/ directory if it does not exist", async () => {
         const { writeManifest } = await import("../manifest.js");