diff --git a/src/commands/init.ts b/src/commands/init.ts
index e7587ef..9a77b64 100644
--- a/src/commands/init.ts
+++ b/src/commands/init.ts
@@ -1,10 +1,12 @@
 import { existsSync } from "node:fs";
-import { mkdir, writeFile } from "node:fs/promises";
+import { mkdir, writeFile, readFile, appendFile } from "node:fs/promises";
 import { join } from "node:path";
 import { CHANGES_DIR, ARCHIVE_DIR, RUNE_DIR, CONFIG_FILE } from "../types.ts";
 import { injectOpenCode } from "../adapters/opencode.ts";
 import { injectClaudeCode } from "../adapters/claude-code.ts";
 import { CommandError } from "../cli/errors.ts";
+import { detectCommandPrefix, getPmPrefix } from "../core/pm.ts";
+import { parse as parseYaml } from "yaml";
 
 const CONFIG_TEMPLATE = `# Rune 配置文件
 # 
@@ -38,11 +40,29 @@ const CONFIG_TEMPLATE = `# Rune 配置文件
 #           # {{change-name}} 任务清单
 `;
 
-export const SUPPORTED_TOOLS: Record<string, (root: string) => Promise<void>> = {
+export const SUPPORTED_TOOLS: Record<string, (root: string, command?: string) => Promise<void>> = {
   opencode: injectOpenCode,
   "claude-code": injectClaudeCode,
 };
 
+async function ensureMetadataCommand(configPath: string, command: string): Promise<void> {
+  const content = await readFile(configPath, "utf-8");
+  const parsed = parseYaml(content) as { metadata?: { command?: string } } | null;
+  if (parsed?.metadata?.command) return;
+
+  if (parsed?.metadata) {
+    const lines = content.split("\n");
+    const metaIdx = lines.findIndex((l) => l.trim() === "metadata:");
+    if (metaIdx >= 0) {
+      lines.splice(metaIdx + 1, 0, `  command: "${command}"`);
+      await writeFile(configPath, lines.join("\n"), "utf-8");
+      return;
+    }
+  }
+
+  await appendFile(configPath, `\nmetadata:\n  command: "${command}"\n`);
+}
+
 export async function runInit(projectRoot: string, tools: string[]): Promise<void> {
   for (const tool of tools) {
     if (!SUPPORTED_TOOLS[tool]) {
@@ -62,7 +82,13 @@ export async function runInit(projectRoot: string, tools: string[]): Promise<voi
     await writeFile(configPath, CONFIG_TEMPLATE, "utf-8");
   }
 
+  const command = await detectCommandPrefix();
+  if (command) {
+    await ensureMetadataCommand(configPath, command);
+  }
+
+  const prefix = command ?? getPmPrefix();
   for (const tool of tools) {
-    await SUPPORTED_TOOLS[tool](projectRoot);
+    await SUPPORTED_TOOLS[tool](projectRoot, prefix === "rune" ? undefined : prefix);
   }
 }
diff --git a/tests/commands/init.test.ts b/tests/commands/init.test.ts
index da381d6..64b13da 100644
--- a/tests/commands/init.test.ts
+++ b/tests/commands/init.test.ts
@@ -41,13 +41,13 @@ describe("runInit", () => {
     expect(existsSync(join(TMP_DIR, ".opencode", "skills", "rune-discuss", "SKILL.md"))).toBe(true);
   });
 
-  it("重复 init 不覆盖 config.yaml", async () => {
+  it("重复 init 不覆盖 config.yaml 已有内容", async () => {
     await runInit(TMP_DIR, ["opencode"]);
     await writeFile(join(TMP_DIR, ".rune", "config.yaml"), "自定义内容");
 
     await runInit(TMP_DIR, ["opencode"]);
     const content = await readFile(join(TMP_DIR, ".rune", "config.yaml"), "utf-8");
-    expect(content).toBe("自定义内容");
+    expect(content).toContain("自定义内容");
   });
 
   it("不支持的工具名抛出 CommandError", async () => {
@@ -59,4 +59,12 @@ describe("runInit", () => {
       expect((e as CommandError).message).toContain("不支持的工具: unknown-tool");
     }
   });
+
+  it("首次 init 时 config.yaml 包含 metadata.command", async () => {
+    await runInit(TMP_DIR, ["opencode"]);
+
+    const content = await readFile(join(TMP_DIR, ".rune", "config.yaml"), "utf-8");
+    expect(content).toContain("metadata:");
+    expect(content).toContain("command:");
+  });
 });