harnessed 3.0.0 → 3.0.2

package/dist/cli.mjs

@@ -793,7 +793,7 @@ var init_resume = __esm({
 
 // package.json
 var package_default = {
-  version: "3.0.0"};
+  version: "3.0.2"};
 
 // src/manifest/errors.ts
 function instancePathToKeyPath(instancePath) {
@@ -2940,7 +2940,12 @@ function validateNonInteractiveFlags(raw, cmdName) {
 
 // src/cli/execute-task.ts
 function registerExecuteTask(program2) {
-  program2.command("execute-task").description("Run execute-task workflow (4-phase chain \u2192 ralph-loop COMPLETE)").requiredOption("--task <text>", "task description (required)").option("--workflow <name>", "workflow name", "execute-task").option("--apply", "execute the spawn (default: dry-run preview)").option("--dry-run", "force dry-run (overrides --apply if both set)").option("--non-interactive", "CI / scripts \u2014 requires --apply or --dry-run").option("--model <model>", "subagent model: 'haiku' | 'sonnet' | 'opus'").option("--model-tier <tier>", "override: 'inherit' bypasses per-phase phase.model (B-10)").option("--max-iterations <n>", "ralph-loop max iter (default 20)", (v) => parseInt(v, 10)).action(async (raw) => {
+  program2.command("execute-task").description(
+    "Run execute-task workflow (4-phase chain \u2192 ralph-loop COMPLETE; immediate by default \u2014 use --dry-run for preview)"
+  ).requiredOption("--task <text>", "task description (required)").option("--workflow <name>", "workflow name", "execute-task").option(
+    "--apply",
+    "(deprecated; kept for backward compat \u2014 execute-task spawns immediately by default)"
+  ).option("--dry-run", "preview only \u2014 do not spawn subagent (opt-in for advanced users)").option("--non-interactive", "CI / scripts \u2014 requires --apply or --dry-run").option("--model <model>", "subagent model: 'haiku' | 'sonnet' | 'opus'").option("--model-tier <tier>", "override: 'inherit' bypasses per-phase phase.model (B-10)").option("--max-iterations <n>", "ralph-loop max iter (default 20)", (v) => parseInt(v, 10)).action(async (raw) => {
     validateNonInteractiveFlags(raw, "execute-task --task <text>");
     if (!raw.task) {
       console.error("error: --task <text> is required");
@@ -2963,7 +2968,7 @@ function registerExecuteTask(program2) {
       };
     }
     const taskCtx = { task: raw.task, task_type: "execute-task" };
-    const isDryRun = raw.dryRun === true || !raw.apply && !raw.nonInteractive;
+    const isDryRun = raw.dryRun === true;
     if (isDryRun) {
       console.log(
         JSON.stringify({ workflow: phases.workflow, phases: phases.phases, taskCtx }, null, 2)
@@ -3041,8 +3046,10 @@ async function dirSizeKb(dir) {
   return Math.round(total / 1024);
 }
 function registerGc(program2) {
-  program2.command("gc").description("Garbage-collect old backup snapshots (dry-run by default)").option("--older-than <duration>", "delete snapshots older than (e.g. 30d / 24h / 4w)", "30d").option("--keep-last <N>", "always keep the most recent N snapshots", "0").option("--apply", "actually delete (default: dry-run preview only)").option("--dry-run", "force dry-run (overrides --apply)").action(async (opts) => {
-    const dryRun = opts.dryRun === true || opts.apply !== true;
+  program2.command("gc").description(
+    "Garbage-collect old backup snapshots (immediate by default \u2014 use --dry-run for preview)"
+  ).option("--older-than <duration>", "delete snapshots older than (e.g. 30d / 24h / 4w)", "30d").option("--keep-last <N>", "always keep the most recent N snapshots", "0").option("--apply", "(deprecated; kept for backward compat \u2014 gc deletes immediately by default)").option("--dry-run", "preview only \u2014 do not delete (opt-in for advanced users)").action(async (opts) => {
+    const dryRun = opts.dryRun === true;
     const olderMs = parseDuration(opts.olderThan ?? "30d");
     if (olderMs == null) {
       console.error(
@@ -3092,7 +3099,7 @@ function registerGc(program2) {
       console.log(`  ${c.ts}  ${c.manifest}  (${c.sizeKb} KB)`);
       if (!dryRun) await rm(c.path, { recursive: true, force: true });
     }
-    if (dryRun) console.log("\n(dry-run \u2014 re-run with --apply to actually delete)");
+    if (dryRun) console.log("\n(dry-run \u2014 re-run without --dry-run to actually delete)");
   });
 }
 async function confirmAt(level, ctx) {
@@ -3397,6 +3404,9 @@ function runArgs(claudeArgs, cwd, timeoutMs = 15e3) {
     });
   });
 }
+function getMcpSpawnCwd() {
+  return homedir();
+}
 
 // src/installers/ccPluginMarketplace.ts
 function parseCmd(cmd) {
@@ -3448,8 +3458,8 @@ var installCcPluginMarketplace = async (ctx) => {
       }
     };
   }
-  const pluginName = parsed.pluginAtMkt.split("@")[0];
-  const installArgs = ["plugin", "install", parsed.pluginAtMkt, "--scope", "project"];
+  const pluginName = parsed.pluginAtMkt.split("@")[0] ?? parsed.pluginAtMkt;
+  const installArgs = ["plugin", "install", parsed.pluginAtMkt, "--scope", "user"];
   const allArgs = [];
   if (parsed.marketplaceRef !== null) {
     allArgs.push(["plugin", "marketplace", "add", parsed.marketplaceRef]);
@@ -3457,30 +3467,30 @@ var installCcPluginMarketplace = async (ctx) => {
   allArgs.push(installArgs);
   for (const argSet of allArgs) {
     for (const a of argSet) {
-      const violation2 = checkCmdString(a);
-      if (violation2) {
+      const violation = checkCmdString(a);
+      if (violation) {
         return {
           ok: false,
           phase: "preflight",
           error: err(
             ctx,
             "/spec/install/cmd",
-            `shell escape detected in constructed cc-plugin arg '${a.slice(0, 60)}': ${violation2.label} (${violation2.hint})`,
+            `shell escape detected in constructed cc-plugin arg '${a.slice(0, 60)}': ${violation.label} (${violation.hint})`,
             "security-gate-bypass"
           )
         };
       }
     }
   }
-  const settingsFile = `${ctx.cwd}/.claude/settings.json`;
+  const settingsFile = `${getMcpSpawnCwd()}/.claude.json`;
   const newEntry = JSON.stringify({ enabledPlugins: { [parsed.pluginAtMkt]: true } }, null, 2);
   const plan = {
     files: [
       {
         target: settingsFile,
-        scope: "PROJECT",
+        scope: "HOME",
         oldText: "",
-        newText: `// will be merged into .claude/settings.json enabledPlugins map by \`claude plugin install\`:
+        newText: `// will be merged into ~/.claude.json enabledPlugins map by \`claude plugin install --scope user\`:
 ${newEntry}
 `
       }
@@ -3495,15 +3505,13 @@ ${newEntry}
   if (ctx.opts.dryRun) return { aborted: true, reason: "user-cancel" };
   const bk = await backup(plan, ctx);
   if (!bk.ok) return { ok: false, phase: "preflight", error: bk.error };
+  const spawnCwd = install.cwd ?? getMcpSpawnCwd();
   let stepOneStderr = "";
   if (parsed.marketplaceRef !== null) {
-    const r1 = await runArgs(
-      ["plugin", "marketplace", "add", parsed.marketplaceRef],
-      install.cwd ?? ctx.cwd
-    );
+    const r1 = await runArgs(["plugin", "marketplace", "add", parsed.marketplaceRef], spawnCwd);
     stepOneStderr = r1.stderr;
   }
-  const r2 = await runArgs(installArgs, install.cwd ?? ctx.cwd);
+  const r2 = await runArgs(installArgs, spawnCwd);
   if (r2.exitCode !== 0) {
     return {
       ok: false,
@@ -3517,43 +3525,34 @@ ${newEntry}
       )
     };
   }
-  const verifyShell = process.platform === "win32" ? "cmd.exe" : "/bin/sh";
-  const verifyFlag = process.platform === "win32" ? "/c" : "-c";
-  const verifyLine = `claude plugin list --json | grep -q ${pluginName}`;
-  const violation = checkCmdString(verifyLine);
-  if (violation) {
-    return {
-      ok: false,
-      phase: "verify",
-      backupId: bk.backupId,
-      error: err(
-        ctx,
-        "/spec/verify/cmd",
-        `verify shell escape: ${violation.label}`,
-        "security-gate-bypass"
-      )
-    };
-  }
   const vr = await new Promise((resolve9) => {
-    const child = spawn(verifyShell, [verifyFlag, verifyLine], { cwd: ctx.cwd, windowsHide: true });
+    const child = spawn("claude", ["plugin", "list", "--json"], {
+      cwd: spawnCwd,
+      shell: process.platform === "win32",
+      windowsHide: true
+    });
+    let stdout2 = "";
     let stderr = "";
+    child.stdout?.setEncoding("utf8").on("data", (c) => {
+      stdout2 += c;
+    });
     child.stderr?.setEncoding("utf8").on("data", (c) => {
       stderr += c;
     });
     const timer = setTimeout(() => {
       child.kill("SIGKILL");
-      resolve9({ exitCode: -1, stderr: `${stderr}[timeout]` });
+      resolve9({ exitCode: -1, stderr: `${stderr}[timeout]`, stdout: stdout2 });
     }, 15e3);
     child.on("error", (e) => {
       clearTimeout(timer);
-      resolve9({ exitCode: -1, stderr: e.message });
+      resolve9({ exitCode: -1, stderr: e.message, stdout: stdout2 });
     });
     child.on("close", (code) => {
       clearTimeout(timer);
-      resolve9({ exitCode: code ?? -1, stderr });
+      resolve9({ exitCode: code ?? -1, stderr, stdout: stdout2 });
     });
   });
-  if (vr.exitCode !== 0) {
+  if (vr.exitCode !== 0 || !vr.stdout.includes(pluginName)) {
     return {
       ok: false,
       phase: "verify",
@@ -3561,7 +3560,7 @@ ${newEntry}
       error: err(
         ctx,
         "/spec/verify/cmd",
-        `verify exit ${vr.exitCode}: ${vr.stderr.slice(0, 200)}`,
+        `verify exit ${vr.exitCode} or '${pluginName}' not in plugin list stdout: ${vr.stderr.slice(0, 200)}`,
         "verify-failed"
       )
     };
@@ -3569,8 +3568,9 @@ ${newEntry}
   await updateInstalled(ctx.cwd, ctx.manifest.metadata.name, install.git_ref, "");
   return { ok: true, backupId: bk.backupId, appliedFiles: [settingsFile] };
 };
-var DEFAULT_TIMEOUT_MS = 15e3;
-async function spawnCmd(ctx, cmd, args) {
+var DEFAULT_VERIFY_TIMEOUT_MS = 15e3;
+var DEFAULT_INSTALL_TIMEOUT_MS = 6e4;
+async function spawnCmd(ctx, cmd, args, timeoutMs) {
   const violation = checkCmdString(cmd);
   if (violation) {
     return {
@@ -3587,8 +3587,7 @@ async function spawnCmd(ctx, cmd, args) {
     };
   }
   const installCfg = ctx.manifest.spec.install;
-  const verifyCfg = ctx.manifest.spec.verify;
-  const timeoutMs = verifyCfg.timeout_ms ?? DEFAULT_TIMEOUT_MS;
+  const effectiveTimeoutMs = timeoutMs ?? DEFAULT_INSTALL_TIMEOUT_MS;
   const env = { ...process.env, ...installCfg.env ?? {} };
   const cwd = installCfg.cwd ?? ctx.cwd;
   let child;
@@ -3615,13 +3614,13 @@ async function spawnCmd(ctx, cmd, args) {
         error: {
           file: ctx.manifest.metadata.name,
           path: "/spec/install/cmd",
-          message: `spawn timed out after ${timeoutMs}ms (cmd: ${cmd}); partial stderr: ${stderr.slice(0, 200)}`,
+          message: `spawn timed out after ${effectiveTimeoutMs}ms (cmd: ${cmd}); partial stderr: ${stderr.slice(0, 200)}`,
           line: null,
           column: null,
           keyword: "spawn-timeout"
         }
       });
-    }, timeoutMs);
+    }, effectiveTimeoutMs);
     child.on("error", (err2) => {
       clearTimeout(timer);
       resolve9({
@@ -3767,7 +3766,7 @@ var installGitCloneWithSetup = async (ctx) => {
   if (ctx.opts.dryRun) return { aborted: true, reason: "user-cancel" };
   const bk = await backup(plan, ctx);
   if (!bk.ok) return { ok: false, phase: "preflight", error: bk.error };
-  const sp = await spawnCmd(ctx, install.cmd, []);
+  const sp = await spawnCmd(ctx, install.cmd, [], DEFAULT_INSTALL_TIMEOUT_MS);
   if (!("exitCode" in sp)) return { ...sp, backupId: bk.backupId };
   if (sp.exitCode !== 0) {
     return {
@@ -3809,7 +3808,8 @@ var installGitCloneWithSetup = async (ctx) => {
       )
     };
   }
-  const vr = await spawnCmd(ctx, ctx.manifest.spec.verify.cmd, []);
+  const verifyTimeoutMs = ctx.manifest.spec.verify.timeout_ms ?? DEFAULT_VERIFY_TIMEOUT_MS;
+  const vr = await spawnCmd(ctx, ctx.manifest.spec.verify.cmd, [], verifyTimeoutMs);
   if (!("exitCode" in vr)) return { ...vr, backupId: bk.backupId };
   const expected = ctx.manifest.spec.verify.expected_exit_code ?? 0;
   if (vr.exitCode !== expected) {
@@ -3912,33 +3912,23 @@ var installMcpHttpAdd = async (ctx) => {
       }
     };
   }
-  const addArgs = [
-    "mcp",
-    "add",
-    "--scope",
-    "project",
-    "--transport",
-    "http",
-    ...hdr.flat,
-    name,
-    url
-  ];
+  const addArgs = ["mcp", "add", "--scope", "user", "--transport", "http", ...hdr.flat, name, url];
   for (const a of addArgs) {
-    const violation2 = checkCmdString(a);
-    if (violation2) {
+    const violation = checkCmdString(a);
+    if (violation) {
       return {
         ok: false,
         phase: "preflight",
         error: err(
           ctx,
           "/spec/install/cmd",
-          `shell escape detected in constructed mcp-http-add arg '${a.slice(0, 60)}': ${violation2.label} (${violation2.hint})`,
+          `shell escape detected in constructed mcp-http-add arg '${a.slice(0, 60)}': ${violation.label} (${violation.hint})`,
           "security-gate-bypass"
         )
       };
     }
   }
-  const mcpFile = `${ctx.cwd}/.mcp.json`;
+  const mcpFile = `${getMcpSpawnCwd()}/.claude.json`;
   const headersObj = {};
   for (let i = 0; i < hdr.flat.length; i += 2) {
     const kv = hdr.flat[i + 1];
@@ -3952,9 +3942,9 @@ var installMcpHttpAdd = async (ctx) => {
     files: [
       {
         target: mcpFile,
-        scope: "PROJECT",
+        scope: "HOME",
         oldText: "",
-        newText: `// will be merged into .mcp.json mcpServers map by \`claude mcp add\`:
+        newText: `// will be merged into ~/.claude.json mcpServers map by \`claude mcp add --scope user\`:
 ${newEntry}
 `
       }
@@ -3969,9 +3959,10 @@ ${newEntry}
   if (ctx.opts.dryRun) return { aborted: true, reason: "user-cancel" };
   const bk = await backup(plan, ctx);
   if (!bk.ok) return { ok: false, phase: "preflight", error: bk.error };
-  const r = await runArgs(addArgs, install.cwd ?? ctx.cwd);
+  const spawnCwd = install.cwd ?? getMcpSpawnCwd();
+  const r = await runArgs(addArgs, spawnCwd);
   if (r.exitCode !== 0) {
-    if (r.stderr.includes("already exists in .mcp.json")) {
+    if (r.stderr.includes("already exists")) {
       return { ok: true, alreadyInstalled: true, backupId: bk.backupId };
     }
     return {
@@ -3986,43 +3977,34 @@ ${newEntry}
       )
     };
   }
-  const verifyShell = process.platform === "win32" ? "cmd.exe" : "/bin/sh";
-  const verifyFlag = process.platform === "win32" ? "/c" : "-c";
-  const verifyLine = `claude mcp list | grep -q ${name}`;
-  const violation = checkCmdString(verifyLine);
-  if (violation) {
-    return {
-      ok: false,
-      phase: "verify",
-      backupId: bk.backupId,
-      error: err(
-        ctx,
-        "/spec/verify/cmd",
-        `verify shell escape: ${violation.label}`,
-        "security-gate-bypass"
-      )
-    };
-  }
   const vr = await new Promise((resolve9) => {
-    const child = spawn(verifyShell, [verifyFlag, verifyLine], { cwd: ctx.cwd, windowsHide: true });
+    const child = spawn("claude", ["mcp", "list"], {
+      cwd: spawnCwd,
+      shell: process.platform === "win32",
+      windowsHide: true
+    });
+    let stdout2 = "";
     let stderr = "";
+    child.stdout?.setEncoding("utf8").on("data", (c) => {
+      stdout2 += c;
+    });
     child.stderr?.setEncoding("utf8").on("data", (c) => {
       stderr += c;
     });
     const timer = setTimeout(() => {
       child.kill("SIGKILL");
-      resolve9({ exitCode: -1, stderr: `${stderr}[timeout]` });
+      resolve9({ exitCode: -1, stderr: `${stderr}[timeout]`, stdout: stdout2 });
     }, 15e3);
     child.on("error", (e) => {
       clearTimeout(timer);
-      resolve9({ exitCode: -1, stderr: e.message });
+      resolve9({ exitCode: -1, stderr: e.message, stdout: stdout2 });
     });
     child.on("close", (code) => {
       clearTimeout(timer);
-      resolve9({ exitCode: code ?? -1, stderr });
+      resolve9({ exitCode: code ?? -1, stderr, stdout: stdout2 });
     });
   });
-  if (vr.exitCode !== 0) {
+  if (vr.exitCode !== 0 || !vr.stdout.includes(name)) {
     return {
       ok: false,
       phase: "verify",
@@ -4030,7 +4012,7 @@ ${newEntry}
       error: err(
         ctx,
         "/spec/verify/cmd",
-        `verify exit ${vr.exitCode}: ${vr.stderr.slice(0, 200)}`,
+        `verify exit ${vr.exitCode} or '${name}' not in mcp list stdout: ${vr.stderr.slice(0, 200)}`,
         "verify-failed"
       )
     };
@@ -4066,7 +4048,7 @@ var installMcpStdioAdd = async (ctx) => {
     "mcp",
     "add",
     "--scope",
-    "project",
+    "user",
     "--transport",
     "stdio",
     name,
@@ -4076,21 +4058,21 @@ var installMcpStdioAdd = async (ctx) => {
     `${pkg}@${ver}`
   ];
   for (const a of addArgs) {
-    const violation2 = checkCmdString(a);
-    if (violation2) {
+    const violation = checkCmdString(a);
+    if (violation) {
       return {
         ok: false,
         phase: "preflight",
         error: err(
           ctx,
           "/spec/install/cmd",
-          `shell escape detected in constructed mcp-add arg '${a.slice(0, 60)}': ${violation2.label} (${violation2.hint})`,
+          `shell escape detected in constructed mcp-add arg '${a.slice(0, 60)}': ${violation.label} (${violation.hint})`,
           "security-gate-bypass"
         )
       };
     }
   }
-  const mcpFile = `${ctx.cwd}/.mcp.json`;
+  const mcpFile = `${getMcpSpawnCwd()}/.claude.json`;
   const newEntry = JSON.stringify(
     { [name]: { type: "stdio", command: "npx", args: ["--yes", `${pkg}@${ver}`] } },
     null,
@@ -4100,9 +4082,9 @@ var installMcpStdioAdd = async (ctx) => {
     files: [
       {
         target: mcpFile,
-        scope: "PROJECT",
+        scope: "HOME",
         oldText: "",
-        newText: `// will be merged into .mcp.json mcpServers map by \`claude mcp add\`:
+        newText: `// will be merged into ~/.claude.json mcpServers map by \`claude mcp add --scope user\`:
 ${newEntry}
 `
       }
@@ -4117,9 +4099,10 @@ ${newEntry}
   if (ctx.opts.dryRun) return { aborted: true, reason: "user-cancel" };
   const bk = await backup(plan, ctx);
   if (!bk.ok) return { ok: false, phase: "preflight", error: bk.error };
-  const r = await runArgs(addArgs, install.cwd ?? ctx.cwd);
+  const spawnCwd = install.cwd ?? getMcpSpawnCwd();
+  const r = await runArgs(addArgs, spawnCwd);
   if (r.exitCode !== 0) {
-    if (r.stderr.includes("already exists in .mcp.json")) {
+    if (r.stderr.includes("already exists")) {
       return { ok: true, alreadyInstalled: true, backupId: bk.backupId };
     }
     return {
@@ -4134,43 +4117,34 @@ ${newEntry}
       )
     };
   }
-  const verifyShell = process.platform === "win32" ? "cmd.exe" : "/bin/sh";
-  const verifyFlag = process.platform === "win32" ? "/c" : "-c";
-  const verifyLine = `claude mcp list | grep -q ${name}`;
-  const violation = checkCmdString(verifyLine);
-  if (violation) {
-    return {
-      ok: false,
-      phase: "verify",
-      backupId: bk.backupId,
-      error: err(
-        ctx,
-        "/spec/verify/cmd",
-        `verify shell escape: ${violation.label}`,
-        "security-gate-bypass"
-      )
-    };
-  }
   const vr = await new Promise((resolve9) => {
-    const child = spawn(verifyShell, [verifyFlag, verifyLine], { cwd: ctx.cwd, windowsHide: true });
+    const child = spawn("claude", ["mcp", "list"], {
+      cwd: spawnCwd,
+      shell: process.platform === "win32",
+      windowsHide: true
+    });
+    let stdout2 = "";
     let stderr = "";
+    child.stdout?.setEncoding("utf8").on("data", (c) => {
+      stdout2 += c;
+    });
     child.stderr?.setEncoding("utf8").on("data", (c) => {
       stderr += c;
     });
     const timer = setTimeout(() => {
       child.kill("SIGKILL");
-      resolve9({ exitCode: -1, stderr: `${stderr}[timeout]` });
+      resolve9({ exitCode: -1, stderr: `${stderr}[timeout]`, stdout: stdout2 });
     }, 15e3);
     child.on("error", (e) => {
       clearTimeout(timer);
-      resolve9({ exitCode: -1, stderr: e.message });
+      resolve9({ exitCode: -1, stderr: e.message, stdout: stdout2 });
     });
     child.on("close", (code) => {
       clearTimeout(timer);
-      resolve9({ exitCode: code ?? -1, stderr });
+      resolve9({ exitCode: code ?? -1, stderr, stdout: stdout2 });
     });
   });
-  if (vr.exitCode !== 0) {
+  if (vr.exitCode !== 0 || !vr.stdout.includes(name)) {
     return {
       ok: false,
       phase: "verify",
@@ -4178,7 +4152,7 @@ ${newEntry}
       error: err(
         ctx,
         "/spec/verify/cmd",
-        `verify exit ${vr.exitCode}: ${vr.stderr.slice(0, 200)}`,
+        `verify exit ${vr.exitCode} or '${name}' not in mcp list stdout: ${vr.stderr.slice(0, 200)}`,
         "verify-failed"
       )
     };
@@ -4244,7 +4218,7 @@ var installNpmCli = async (ctx) => {
   if (ctx.opts.dryRun) return { aborted: true, reason: "user-cancel" };
   const bk = await backup(plan, ctx);
   if (!bk.ok) return { ok: false, phase: "preflight", error: bk.error };
-  const sp = await spawnCmd(ctx, cmd, []);
+  const sp = await spawnCmd(ctx, cmd, [], DEFAULT_INSTALL_TIMEOUT_MS);
   if (!("exitCode" in sp)) return { ...sp, backupId: bk.backupId };
   if (sp.exitCode !== 0) {
     return {
@@ -4259,7 +4233,8 @@ var installNpmCli = async (ctx) => {
       )
     };
   }
-  const vr = await spawnCmd(ctx, ctx.manifest.spec.verify.cmd, []);
+  const verifyTimeoutMs = ctx.manifest.spec.verify.timeout_ms ?? DEFAULT_VERIFY_TIMEOUT_MS;
+  const vr = await spawnCmd(ctx, ctx.manifest.spec.verify.cmd, [], verifyTimeoutMs);
   if (!("exitCode" in vr)) return { ...vr, backupId: bk.backupId };
   const expected = ctx.manifest.spec.verify.expected_exit_code ?? 0;
   if (vr.exitCode !== expected) {
@@ -4360,7 +4335,7 @@ var installNpxSkillInstaller = async (ctx) => {
   if (ctx.opts.dryRun) return { aborted: true, reason: "user-cancel" };
   const bk = await backup(plan, ctx);
   if (!bk.ok) return { ok: false, phase: "preflight", error: bk.error };
-  const sp = await spawnCmd(ctx, install.cmd, []);
+  const sp = await spawnCmd(ctx, install.cmd, [], DEFAULT_INSTALL_TIMEOUT_MS);
   if (!("exitCode" in sp)) return { ...sp, backupId: bk.backupId };
   if (sp.exitCode !== 0) {
     return {
@@ -4393,7 +4368,8 @@ var installNpxSkillInstaller = async (ctx) => {
       }
     };
   }
-  const vr = await spawnCmd(ctx, ctx.manifest.spec.verify.cmd, []);
+  const verifyTimeoutMs = ctx.manifest.spec.verify.timeout_ms ?? DEFAULT_VERIFY_TIMEOUT_MS;
+  const vr = await spawnCmd(ctx, ctx.manifest.spec.verify.cmd, [], verifyTimeoutMs);
   if (!("exitCode" in vr)) return { ...vr, backupId: bk.backupId };
   const expected = ctx.manifest.spec.verify.expected_exit_code ?? 0;
   if (vr.exitCode !== expected) {
@@ -4465,7 +4441,7 @@ function formatError(e) {
   return `${head}${where}${tip}`;
 }
 function registerInstall(program2) {
-  program2.command("install <name>").description("Install an upstream (dry-run by default \u2014 pass --apply to execute)").option("--apply", "execute the install (default: dry-run preview only)").option("--dry-run", "force dry-run (overrides --apply if both are set)").option("--system", "allow L4 system-wide install (e.g. global npm install)").option("--non-interactive", "skip all prompts (CI / scripts) \u2014 requires --apply or --dry-run").option("--full-diff", "expand diffs longer than 200 lines").option("--no-color", "disable ANSI colors (auto-detected when piped)").option(
+  program2.command("install <name>").description("Install an upstream (immediate by default \u2014 use --dry-run for preview)").option("--apply", "(deprecated; kept for backward compat \u2014 install is immediate by default)").option("--dry-run", "preview only \u2014 do not write to disk (opt-in for advanced users)").option("--system", "allow L4 system-wide install (e.g. global npm install)").option("--non-interactive", "skip all prompts (CI / scripts) \u2014 requires --apply or --dry-run").option("--full-diff", "expand diffs longer than 200 lines").option("--no-color", "disable ANSI colors (auto-detected when piped)").option(
     "--known-good",
     "use known-good version lock from versions/<harnessed-ver>-known-good.yaml"
   ).action(async (name, raw) => {
@@ -4497,9 +4473,10 @@ function registerInstall(program2) {
       console.error(`  fix:  run 'harnessed audit' to inspect manifest issues`);
       process.exit(1);
     }
+    const dryRun = raw.dryRun === true;
     const opts = {
-      apply: raw.apply === true,
-      dryRun: raw.dryRun === true,
+      apply: !dryRun,
+      dryRun,
       system: raw.system === true,
       nonInteractive: raw.nonInteractive === true,
       fullDiff: raw.fullDiff === true,
@@ -4545,11 +4522,17 @@ async function listBaseManifests(cwd) {
   return out;
 }
 function registerInstallBase(program2) {
-  program2.command("install-base").description("Install the phase 1.3 base profile (auto-glob manifests; dry-run by default)").option("--apply", "execute the install (default: dry-run preview only)").option("--dry-run", "force dry-run (overrides --apply if both are set)").option("--non-interactive", "skip all prompts (CI / scripts) \u2014 requires --apply or --dry-run").action(async (raw) => {
+  program2.command("install-base").description(
+    "Install the phase 1.3 base profile (immediate by default \u2014 use --dry-run for preview)"
+  ).option(
+    "--apply",
+    "(deprecated; kept for backward compat \u2014 install-base is immediate by default)"
+  ).option("--dry-run", "preview only \u2014 do not write to disk (opt-in for advanced users)").option("--non-interactive", "skip all prompts (CI / scripts) \u2014 requires --apply or --dry-run").action(async (raw) => {
     validateNonInteractiveFlags(raw, "install-base");
+    const dryRun = raw.dryRun === true;
     const opts = {
-      apply: raw.apply === true,
-      dryRun: raw.dryRun === true,
+      apply: !dryRun,
+      dryRun,
       system: false,
       nonInteractive: raw.nonInteractive === true,
       fullDiff: false,
@@ -4609,7 +4592,12 @@ function basename(upstream) {
   return (upstream.split("/").pop() ?? upstream).replace(/\.git$/, "");
 }
 function registerManifestAdd(program2) {
-  program2.command("manifest-add <upstream>").description("Add a new upstream adapter (EE-5 5-question merge gate, D-03 BOTH dry-run/apply)").option("--category <cat>", "manifest category (skill-packs | tools)", "skill-packs").option("--name <name>", "short adapter name (defaults to <upstream> basename)").option("--apply", "persist EE-5 answers (default: dry-run preview)").option("--dry-run", "force dry-run (overrides --apply if both set)").option("--non-interactive", "CI/scripts \u2014 requires --apply or --dry-run; WARN-only dry-run").action(async (upstream, raw) => {
+  program2.command("manifest-add <upstream>").description(
+    "Add a new upstream adapter (EE-5 5-question merge gate; immediate by default \u2014 use --dry-run for preview)"
+  ).option("--category <cat>", "manifest category (skill-packs | tools)", "skill-packs").option("--name <name>", "short adapter name (defaults to <upstream> basename)").option(
+    "--apply",
+    "(deprecated; kept for backward compat \u2014 manifest-add persists immediately by default)"
+  ).option("--dry-run", "preview only \u2014 do not write JSON (opt-in for advanced users)").option("--non-interactive", "CI/scripts \u2014 requires --apply or --dry-run; WARN-only dry-run").action(async (upstream, raw) => {
     validateNonInteractiveFlags(raw, "manifest-add <upstream>");
     const name = raw.name ?? basename(upstream);
     const category = raw.category ?? "skill-packs";
@@ -4638,7 +4626,8 @@ function registerManifestAdd(program2) {
       payload[f] = a;
     }
     rl.close();
-    if (raw.apply) {
+    const dryRun = raw.dryRun === true;
+    if (!dryRun) {
       writeFileSync(outPath, `${JSON.stringify(payload, null, 2)}
 `, "utf8");
       console.log(`[manifest-add] EE-5 gate passed; wrote ${outPath}`);
@@ -4652,14 +4641,19 @@ function registerManifestAdd(program2) {
 
 // src/cli/research.ts
 function registerResearch(program2) {
-  program2.command("research").description("Run research workflow (search category sub-routing \u2192 spawn \u2192 verbatim COMPLETE)").requiredOption("--query <text>", "research prompt (required)").option("--apply", "execute the spawn (default: dry-run preview only)").option("--dry-run", "force dry-run (overrides --apply if both are set)").option("--non-interactive", "skip all prompts (CI / scripts) \u2014 requires --apply or --dry-run").option("--model <model>", "subagent model: 'haiku' | 'sonnet' | 'opus'").action(async (raw) => {
+  program2.command("research").description(
+    "Run research workflow (search category sub-routing \u2192 spawn \u2192 verbatim COMPLETE; immediate by default \u2014 use --dry-run for preview)"
+  ).requiredOption("--query <text>", "research prompt (required)").option(
+    "--apply",
+    "(deprecated; kept for backward compat \u2014 research spawns immediately by default)"
+  ).option("--dry-run", "preview only \u2014 do not spawn subagent (opt-in for advanced users)").option("--non-interactive", "skip all prompts (CI / scripts) \u2014 requires --apply or --dry-run").option("--model <model>", "subagent model: 'haiku' | 'sonnet' | 'opus'").action(async (raw) => {
     validateNonInteractiveFlags(raw, "research --query <text>");
     if (!raw.query) {
       console.error("error: --query <text> is required");
       process.exit(2);
     }
     const taskCtx = { task: raw.query, task_type: "search" };
-    if (raw.dryRun === true || !raw.apply && !raw.nonInteractive) {
+    if (raw.dryRun === true) {
       const preview = await runRouting(taskCtx, {
         skillsRoot: void 0,
         // Stub spawn — dry-run never reaches it; explicit COMPLETE keeps shape happy.
@@ -4677,7 +4671,9 @@ function registerResearch(program2) {
       }
       console.log(`[dry-run] matched_rule: ${preview.matchedRule?.id ?? "(fallback supervisor)"}`);
       console.log(`[dry-run] query: ${raw.query}`);
-      console.log("  (use --apply to spawn the subagent and emit verbatim COMPLETE round-trip)");
+      console.log(
+        "  (run without --dry-run to spawn the subagent and emit verbatim COMPLETE round-trip)"
+      );
       process.exit(0);
     }
     const result = await runRouting(taskCtx, {
@@ -4869,7 +4865,7 @@ async function warnIfAgentTeamsMissing() {
   console.warn("\n\u26A0\uFE0F  Agent Teams \u672A\u542F\u7528 \u2014 parallelism-gate \u5347\u7EA7\u8DEF\u5F84\u4E0D\u53EF\u7528");
   console.warn("   \u4FEE\u590D: claude config set env.CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS 1");
   console.warn(
-    "   \u8BF4\u660E: harnessed v2.0 \u4E09\u5C42\u6808\u65B9\u6CD5\u8BBA parallelism-gate \u5347\u7EA7\u8DEF\u5F84\u9700 CC 2.1.133+ Agent Teams enable (sister ~/.claude/rules/agent-teams.md)"
+    "   \u8BF4\u660E: harnessed v3.0 \u4E09\u5C42\u6808\u65B9\u6CD5\u8BBA parallelism-gate \u5347\u7EA7\u8DEF\u5F84\u9700 CC 2.1.133+ Agent Teams enable"
   );
   console.warn(
     "   \u4E0D\u963B\u585E setup,\u540E\u7EED parallelism-gate workflow phase \u89E6\u53D1\u65F6\u81EA\u52A8\u964D\u7EA7 subagent fan-out\n"
@@ -5025,7 +5021,7 @@ MCP servers configured. Run \`/mcp\` in Claude Code to verify each server's conn
       );
     }
     console.log(
-      "\n\u2713 harnessed v2.0 \u4E09\u5C42\u6808\u65B9\u6CD5\u8BBA bundled \u2014 4 workflows + 6 judgments + 37 capabilities ready"
+      "\n\u2713 harnessed v3.0 \u4E09\u5C42\u6808\u65B9\u6CD5\u8BBA bundled \u2014 23 workflows (4 master + 18 sub + 1 standalone) + 6 disciplines + 10 judgments + ~83 capabilities ready"
     );
     console.log(
       "  workflows in <packageRoot>/workflows/ (Pure bundled, NOT user-dir override per D-01)"
@@ -5320,12 +5316,12 @@ async function runUninstall(manifest, opts) {
 
 // src/cli/uninstall.ts
 function registerUninstall(program2) {
-  program2.command("uninstall <name>").description("Uninstall an upstream (dry-run by default \u2014 pass --apply to execute)").option("--apply", "execute the uninstall (default: dry-run preview only)").option("--dry-run", "force dry-run (overrides --apply if both are set)").option("--yes", "skip interactive confirm \u2014 requires --apply (CI / scripts)").option("--non-interactive", "alias for --yes (CI compat)").action(async (name, raw) => {
+  program2.command("uninstall <name>").description("Uninstall an upstream (immediate by default \u2014 use --dry-run for preview)").option("--apply", "(deprecated; kept for backward compat \u2014 uninstall is immediate by default)").option("--dry-run", "preview only \u2014 do not delete files (opt-in for advanced users)").option("--yes", "skip interactive confirm (CI / scripts) \u2014 fatal with --dry-run").option("--non-interactive", "alias for --yes (CI compat)").action(async (name, raw) => {
     const yes = raw.yes === true || raw.nonInteractive === true;
-    if (yes && !raw.apply) {
+    if (yes && raw.dryRun) {
       console.error(
-        `error: --yes requires --apply to execute
-  fix:  harnessed uninstall ${name} --yes --apply`
+        `error: --yes is incompatible with --dry-run (dry-run does not mutate)
+  fix:  harnessed uninstall ${name} --yes  (immediate) OR harnessed uninstall ${name} --dry-run  (preview)`
       );
       process.exit(2);
     }
@@ -5356,10 +5352,10 @@ function registerUninstall(program2) {
       process.exit(1);
     }
     const method = v.manifest.spec.install.method;
-    const dryRun = raw.dryRun === true || !raw.apply;
+    const dryRun = raw.dryRun === true;
     if (dryRun) {
       console.log(`[dry-run] would uninstall '${resolvedName}' via method '${method}'`);
-      console.log(`  run with --apply to execute`);
+      console.log(`  run without --dry-run to execute`);
       process.exit(2);
     }
     if (!yes) {