sequant 1.3.1 → 1.5.0

package/README.md

@@ -45,6 +45,8 @@ When using AI coding assistants, work can become scattered and quality inconsist
 | Git | `git --version` | Required |
 | [jq](https://jqlang.github.io/jq/) | `jq --version` | Optional, improves hook performance |
 
+> **Note:** Sequant currently requires GitHub for issue tracking. GitLab and Bitbucket support is planned for a future release. See [Platform Requirements](docs/platform-requirements.md) for workarounds if you use a different platform.
+
 ### Setup
 
 ```bash
@@ -309,10 +311,16 @@ Configure `sequant run` defaults in `.sequant/settings.json`:
     "qualityLoop": false,
     "maxIterations": 3,
     "smartTests": true
+  },
+  "agents": {
+    "parallel": false,
+    "model": "haiku"
   }
 }
 ```
 
+#### Run Settings
+
 | Option | Default | Description |
 |--------|---------|-------------|
 | `logJson` | `true` | Enable JSON logging for run sessions |
@@ -324,6 +332,29 @@ Configure `sequant run` defaults in `.sequant/settings.json`:
 | `maxIterations` | `3` | Max quality loop iterations |
 | `smartTests` | `true` | Auto-detect test commands |
 
+#### Agent Settings
+
+| Option | Default | Description |
+|--------|---------|-------------|
+| `parallel` | `false` | Run sub-agents in parallel (faster but higher token usage) |
+| `model` | `"haiku"` | Default model for sub-agents (`haiku`, `sonnet`, or `opus`) |
+
+##### Cost vs Speed Trade-offs
+
+Skills like `/qa`, `/merger`, and `/fullsolve` spawn sub-agents for quality checks. The `agents` settings control how these agents execute:
+
+| Mode | Token Usage | Speed | Best For |
+|------|-------------|-------|----------|
+| Sequential (`parallel: false`) | 1x (baseline) | Slower | Limited API plans, cost-conscious users |
+| Parallel (`parallel: true`) | ~2-3x | ~50% faster | Unlimited plans, batch operations |
+
+**Override per invocation:**
+
+```bash
+/qa 123 --parallel     # Force parallel (faster)
+/qa 123 --sequential   # Force sequential (cheaper)
+```
+
 CLI flags override settings file values.
 
 ## Directory Structure
@@ -352,6 +383,7 @@ After `sequant init`:
 - [Run Command](docs/run-command.md) — Batch execution options
 - [Customization Guide](docs/customization.md) — Override templates safely
 - [MCP Integrations](docs/mcp-integrations.md) — Optional MCP server setup
+- [Platform Requirements](docs/platform-requirements.md) — GitHub dependency and workarounds
 - [Troubleshooting](docs/troubleshooting.md) — Common issues and solutions
 - [Testing Guide](docs/testing.md) — Cross-platform testing matrix
 - [Git Patterns](docs/git-patterns.md) — Worktree and merge workflows

package/dist/bin/cli.js

@@ -55,6 +55,7 @@ program
     .option("-y, --yes", "Skip confirmation prompts")
     .option("-f, --force", "Overwrite existing configuration")
     .option("-i, --interactive", "Force interactive mode even in non-TTY environment")
+    .option("--skip-setup", "Skip the dependency setup wizard")
     .action(initCommand);
 program
     .command("update")

package/dist/bin/cli.js.map

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package/dist/src/commands/doctor.d.ts

@@ -1,8 +1,5 @@
 /**
  * sequant doctor - Check installation health
  */
-interface DoctorOptions {
-}
-export declare function doctorCommand(options: DoctorOptions): Promise<void>;
-export {};
+export declare function doctorCommand(): Promise<void>;
 //# sourceMappingURL=doctor.d.ts.map

package/dist/src/commands/doctor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;GAEG;AAqBH,wBAAsB,aAAa,IAAI,OAAO,CAAC,IAAI,CAAC,CA2RnD"}

package/dist/src/commands/doctor.integration.test.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Integration tests for the doctor command
+ *
+ * These tests run the actual CLI as a subprocess to catch runtime errors
+ * that unit tests with mocks might miss (e.g., ESM import issues).
+ *
+ * Issue #60: Unit tests mock all system functions, missing runtime errors
+ */
+export {};
+//# sourceMappingURL=doctor.integration.test.d.ts.map

package/dist/src/commands/doctor.integration.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"doctor.integration.test.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor.integration.test.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG"}

package/dist/src/commands/doctor.integration.test.js

@@ -0,0 +1,71 @@
+/**
+ * Integration tests for the doctor command
+ *
+ * These tests run the actual CLI as a subprocess to catch runtime errors
+ * that unit tests with mocks might miss (e.g., ESM import issues).
+ *
+ * Issue #60: Unit tests mock all system functions, missing runtime errors
+ */
+import { execSync } from "child_process";
+import { describe, it, expect, beforeAll } from "vitest";
+import { resolve, dirname } from "path";
+import { fileURLToPath } from "url";
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const projectRoot = resolve(__dirname, "../..");
+const cliPath = resolve(projectRoot, "dist/bin/cli.js");
+const execOptions = {
+    cwd: projectRoot,
+    encoding: "utf-8",
+    // Capture both stdout and stderr
+    stdio: ["pipe", "pipe", "pipe"],
+};
+describe("doctor command integration", () => {
+    beforeAll(() => {
+        // Build the project before running integration tests
+        execSync("npm run build", {
+            cwd: projectRoot,
+            stdio: "ignore",
+        });
+    }, 30000); // 30 second timeout for build
+    it("runs without crashing", () => {
+        let output;
+        let exitCode = 0;
+        try {
+            output = execSync(`node ${cliPath} doctor`, execOptions);
+        }
+        catch (error) {
+            // execSync throws on non-zero exit codes
+            // We accept exit code 1 (some checks fail) as valid in CI environments
+            const execError = error;
+            exitCode = execError.status;
+            output = execError.stdout || "";
+            // Only exit codes 0 (all pass) and 1 (some checks fail) are acceptable
+            // Any other exit code indicates a crash or uncaught exception
+            if (exitCode !== null && exitCode !== 0 && exitCode !== 1) {
+                throw new Error(`Doctor command crashed with exit code ${exitCode}.\n` +
+                    `stdout: ${execError.stdout}\n` +
+                    `stderr: ${execError.stderr}`);
+            }
+        }
+        // Verify the command actually ran and produced expected output
+        expect(output).toContain("Running health checks");
+        // Accept both exit code 0 (all pass) and 1 (some checks fail in CI)
+        expect([0, 1]).toContain(exitCode);
+    });
+    it("shows help without crashing", () => {
+        let output;
+        try {
+            output = execSync(`node ${cliPath} doctor --help`, execOptions);
+        }
+        catch (error) {
+            const execError = error;
+            throw new Error(`Doctor --help crashed with exit code ${execError.status}.\n` +
+                `stdout: ${execError.stdout}\n` +
+                `stderr: ${execError.stderr}`);
+        }
+        // Verify help output contains expected content
+        expect(output).toContain("doctor");
+        expect(output).toContain("Check your Sequant installation");
+    });
+});
+//# sourceMappingURL=doctor.integration.test.js.map

package/dist/src/commands/doctor.integration.test.js.map

@@ -0,0 +1 @@
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package/dist/src/commands/doctor.js

@@ -5,7 +5,7 @@ import chalk from "chalk";
 import { fileExists, isExecutable } from "../lib/fs.js";
 import { getManifest } from "../lib/manifest.js";
 import { commandExists, isGhAuthenticated, isNativeWindows, isWSL, checkOptionalMcpServers, OPTIONAL_MCP_SERVERS, } from "../lib/system.js";
-export async function doctorCommand(options) {
+export async function doctorCommand() {
     console.log(chalk.blue("\n🔍 Running health checks...\n"));
     const checks = [];
     // Check 1: Manifest exists

package/dist/src/commands/doctor.js.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.js","sourceRoot":"","sources":["../../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AACxD,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EACL,aAAa,EACb,iBAAiB,EACjB,eAAe,EACf,KAAK,EACL,uBAAuB,EACvB,oBAAoB,GACrB,MAAM,kBAAkB,CAAC;AAS1B,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC,CAAC;IAE3D,MAAM,MAAM,GAAY,EAAE,CAAC;IAE3B,2BAA2B;IAC3B,MAAM,QAAQ,GAAG,MAAM,WAAW,EAAE,CAAC;IACrC,IAAI,QAAQ,EAAE,CAAC;QACb,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,kCAAkC,QAAQ,CAAC,OAAO,GAAG;SAC/D,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,qDAAqD;SAC/D,CAAC,CAAC;IACL,CAAC;IAED,4BAA4B;IAC5B,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,gBAAgB,CAAC,CAAC;IACvD,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,QAAQ;YACd,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,yBAAyB;SACnC,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,QAAQ;YACd,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,mCAAmC;SAC7C,CAAC,CAAC;IACL,CAAC;IAED,+BAA+B;IAC/B,MAAM,UAAU,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC;IAC1C,MAAM,aAAa,GAAa,EAAE,CAAC;IACnC,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;QAC/B,IAAI,CAAC,CAAC,MAAM,UAAU,CAAC,kBAAkB,KAAK,WAAW,CAAC,CAAC,EAAE,CAAC;YAC5D,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QAC5B,CAAC;IACH,CAAC;IACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,aAAa;YACnB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,0CAA0C;SACpD,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,aAAa;YACnB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,mBAAmB,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;SACvD,CAAC,CAAC;IACL,CAAC;IAED,2BAA2B;IAC3B,MAAM,UAAU,GAAG,MAAM,UAAU,CAAC,eAAe,CAAC,CAAC;IACrD,IAAI,UAAU,EAAE,CAAC;QACf,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,OAAO;YACb,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,wBAAwB;SAClC,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,OAAO;YACb,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,+CAA+C;SACzD,CAAC,CAAC;IACL,CAAC;IAED,mCAAmC;IACnC,MAAM,WAAW,GAAG,2BAA2B,CAAC;IAChD,IAAI,MAAM,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;QAClC,IAAI,MAAM,YAAY,CAAC,WAAW,CAAC,EAAE,CAAC;YACpC,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,kBAAkB;gBACxB,MAAM,EAAE,MAAM;gBACd,OAAO,EAAE,6BAA6B;aACvC,CAAC,CAAC;QACL,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,kBAAkB;gBACxB,MAAM,EAAE,MAAM;gBACd,OAAO,EACL,gEAAgE;aACnE,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,yBAAyB;IACzB,MAAM,aAAa,GAAG,MAAM,UAAU,CAAC,uBAAuB,CAAC,CAAC;IAChE,IAAI,aAAa,EAAE,CAAC;QAClB,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,sBAAsB;SAChC,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,6CAA6C;SACvD,CAAC,CAAC;IACL,CAAC;IAED,oBAAoB;IACpB,MAAM,SAAS,GAAG,MAAM,UAAU,CAAC,MAAM,CAAC,CAAC;IAC3C,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,gBAAgB;YACtB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,yBAAyB;SACnC,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,gBAAgB;YACtB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,qDAAqD;SAC/D,CAAC,CAAC;IACL,CAAC;IAED,gCAAgC;IAChC,IAAI,aAAa,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,YAAY;YAClB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,qBAAqB;SAC/B,CAAC,CAAC;QAEH,wDAAwD;QACxD,IAAI,iBAAiB,EAAE,EAAE,CAAC;YACxB,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,aAAa;gBACnB,MAAM,EAAE,MAAM;gBACd,OAAO,EAAE,yBAAyB;aACnC,CAAC,CAAC;QACL,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,aAAa;gBACnB,MAAM,EAAE,MAAM;gBACd,OAAO,EAAE,+CAA+C;aACzD,CAAC,CAAC;QACL,CAAC;IACH,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,YAAY;YAClB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,oDAAoD;SAC9D,CAAC,CAAC;IACL,CAAC;IAED,iDAAiD;IACjD,IAAI,aAAa,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC5B,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,iBAAiB;YACvB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,yBAAyB;SACnC,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,iBAAiB;YACvB,MAAM,EAAE,MAAM;YACd,OAAO,EACL,gFAAgF;SACnF,CAAC,CAAC;IACL,CAAC;IAED,oDAAoD;IACpD,IAAI,aAAa,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,IAAI;YACV,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,gDAAgD;SAC1D,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,IAAI;YACV,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,2DAA2D;SACrE,CAAC,CAAC;IACL,CAAC;IAED,uCAAuC;IACvC,IAAI,eAAe,EAAE,EAAE,CAAC;QACtB,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EACL,qFAAqF;SACxF,CAAC,CAAC;IACL,CAAC;SAAM,IAAI,KAAK,EAAE,EAAE,CAAC;QACnB,MAAM,CAAC,IAAI,CAAC;YACV,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,+CAA+C;SACzD,CAAC,CAAC;IACL,CAAC;IACD,4DAA4D;IAE5D,iCAAiC;IACjC,MAAM,SAAS,GAAG,uBAAuB,EAAE,CAAC;IAC5C,MAAM,cAAc,GAAG,oBAAoB,CAAC,MAAM,CAChD,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CACzB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;IACrB,MAAM,WAAW,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IAE3E,IAAI,cAAc,CAAC,MAAM,KAAK,oBAAoB,CAAC,MAAM,EAA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package/dist/src/commands/doctor.test.js

@@ -87,7 +87,7 @@ describe("doctor command", () => {
         it("passes when gh CLI is installed", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("GitHub CLI");
             expect(output).toContain("gh CLI is installed");
@@ -95,7 +95,7 @@ describe("doctor command", () => {
         it("fails when gh CLI is not installed", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "gh");
             mockIsGhAuthenticated.mockReturnValue(false);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("GitHub CLI");
             expect(output).toContain("gh CLI not installed");
@@ -104,7 +104,7 @@ describe("doctor command", () => {
         it("passes when gh CLI is authenticated", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("GitHub Auth");
             expect(output).toContain("gh CLI is authenticated");
@@ -112,7 +112,7 @@ describe("doctor command", () => {
         it("fails when gh CLI is not authenticated", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(false);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("GitHub Auth");
             expect(output).toContain("gh CLI not authenticated");
@@ -120,7 +120,7 @@ describe("doctor command", () => {
         });
         it("skips auth check when gh CLI is not installed", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "gh");
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             // Should not contain auth check result since gh is not installed
             expect(output).not.toContain("GitHub Auth");
@@ -130,7 +130,7 @@ describe("doctor command", () => {
         it("passes when claude CLI is installed", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Claude Code CLI");
             expect(output).toContain("claude CLI is installed");
@@ -138,7 +138,7 @@ describe("doctor command", () => {
         it("fails when claude CLI is not installed", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "claude");
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Claude Code CLI");
             expect(output).toContain("claude CLI not installed");
@@ -148,7 +148,7 @@ describe("doctor command", () => {
         it("shows install link when claude CLI is missing", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "claude");
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("https://docs.anthropic.com/en/docs/claude-code");
         });
@@ -157,7 +157,7 @@ describe("doctor command", () => {
         it("passes when jq is installed", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("jq");
             expect(output).toContain("jq is installed");
@@ -165,7 +165,7 @@ describe("doctor command", () => {
         it("warns when jq is not installed", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "jq");
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("jq");
             expect(output).toContain("jq not installed");
@@ -178,7 +178,7 @@ describe("doctor command", () => {
         it("warns when running on native Windows", async () => {
             mockIsNativeWindows.mockReturnValue(true);
             mockIsWSL.mockReturnValue(false);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Platform");
             expect(output).toContain("native Windows");
@@ -187,7 +187,7 @@ describe("doctor command", () => {
         it("passes when running in WSL", async () => {
             mockIsNativeWindows.mockReturnValue(false);
             mockIsWSL.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Platform");
             expect(output).toContain("Running in WSL");
@@ -196,7 +196,7 @@ describe("doctor command", () => {
         it("does not show platform check on macOS/Linux", async () => {
             mockIsNativeWindows.mockReturnValue(false);
             mockIsWSL.mockReturnValue(false);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             // Should not contain Platform check on non-Windows systems
             expect(output).not.toContain("Platform");
@@ -206,20 +206,20 @@ describe("doctor command", () => {
         it("all checks pass when everything is installed and configured", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("All checks passed");
             expect(processExitSpy).not.toHaveBeenCalled();
         });
         it("exits with failure when gh is missing even if jq is present", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "gh");
-            await doctorCommand({});
+            await doctorCommand();
             expect(processExitSpy).toHaveBeenCalledWith(1);
         });
         it("shows only warnings (no failure) when only jq is missing", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "jq");
             mockIsGhAuthenticated.mockReturnValue(true);
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Warnings:");
             expect(output).toContain("should work");
@@ -233,7 +233,7 @@ describe("doctor command", () => {
                 context7: true,
                 "sequential-thinking": true,
             });
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("MCP Servers");
             expect(output).toContain("All optional MCPs configured");
@@ -244,7 +244,7 @@ describe("doctor command", () => {
                 context7: false,
                 "sequential-thinking": true,
             });
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("MCP Servers");
             expect(output).toContain("Some MCPs configured");
@@ -260,7 +260,7 @@ describe("doctor command", () => {
                 context7: false,
                 "sequential-thinking": false,
             });
-            await doctorCommand({});
+            await doctorCommand();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("MCP Servers");
             expect(output).toContain("No optional MCPs configured");
@@ -274,7 +274,7 @@ describe("doctor command", () => {
                 context7: false,
                 "sequential-thinking": false,
             });
-            await doctorCommand({});
+            await doctorCommand();
             // Should complete without failure
             expect(processExitSpy).not.toHaveBeenCalled();
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");

package/dist/src/commands/doctor.test.js.map

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package/dist/src/commands/init.d.ts

@@ -6,6 +6,7 @@ interface InitOptions {
     yes?: boolean;
     force?: boolean;
     interactive?: boolean;
+    skipSetup?: boolean;
 }
 export declare function initCommand(options: InitOptions): Promise<void>;
 export {};

package/dist/src/commands/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/commands/init.ts"],"names":[],"mappings":"AAAA;;GAEG;AAsDH,UAAU,WAAW;IACnB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AA2CD,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+OrE"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/commands/init.ts"],"names":[],"mappings":"AAAA;;GAEG;AA2DH,UAAU,WAAW;IACnB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAyCD,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAqRrE"}

package/dist/src/commands/init.js

@@ -11,6 +11,7 @@ import { createDefaultSettings } from "../lib/settings.js";
 import { fileExists, ensureDir, readFile, writeFile } from "../lib/fs.js";
 import { commandExists, isGhAuthenticated, getInstallHint, } from "../lib/system.js";
 import { shouldUseInteractiveMode, getNonInteractiveReason, } from "../lib/tty.js";
+import { checkAllDependencies, displayDependencyStatus, runSetupWizard, shouldRunSetupWizard, } from "../lib/wizard.js";
 /**
  * Check prerequisites and display warnings
  */
@@ -46,10 +47,8 @@ const GITIGNORE_ENTRIES = [
 async function updateGitignore() {
     const gitignorePath = ".gitignore";
     let content = "";
-    let existed = false;
     if (await fileExists(gitignorePath)) {
         content = await readFile(gitignorePath);
-        existed = true;
         // Check if already has .sequant/
         if (content.includes(".sequant/")) {
             return false; // Already configured
@@ -77,17 +76,46 @@ export async function initCommand(options) {
         console.log(chalk.yellow(`⚡ Non-interactive mode detected${reason ? ` (${reason})` : ""}`));
         console.log(chalk.gray("   Using defaults. Use --interactive to force prompts.\n"));
     }
-    // Check prerequisites and display warnings
+    // Check dependencies and run setup wizard if needed
+    const depCheckResult = checkAllDependencies();
+    let wizardRemainingIssues = [];
+    if (shouldRunSetupWizard({ skipSetup: options.skipSetup, yes: options.yes })) {
+        // Display dependency status
+        displayDependencyStatus(depCheckResult);
+        // Run wizard if there are missing required dependencies
+        if (depCheckResult.hasMissing) {
+            const wizardResult = await runSetupWizard(depCheckResult, {
+                skipPrompts,
+            });
+            wizardRemainingIssues = wizardResult.remainingIssues;
+        }
+    }
+    else if (options.skipSetup) {
+        // User explicitly skipped - show brief status
+        console.log(chalk.gray("Skipping dependency setup wizard (--skip-setup)\n"));
+    }
+    // Fall back to legacy warning system for any remaining issues
     const { warnings, suggestions } = checkPrerequisites();
-    if (warnings.length > 0) {
-        console.log(chalk.yellow("⚠️  Prerequisites:\n"));
-        for (const warning of warnings) {
-            console.log(chalk.yellow(`   • ${warning}`));
+    // Only show warnings if wizard didn't already handle them or if there are remaining issues
+    if (wizardRemainingIssues.length > 0 ||
+        (options.skipSetup && warnings.length > 0)) {
+        if (wizardRemainingIssues.length > 0) {
+            console.log(chalk.yellow("⚠️  Remaining setup issues:\n"));
+            for (const issue of wizardRemainingIssues) {
+                console.log(chalk.yellow(`   • ${issue}`));
+            }
+            console.log();
         }
-        for (const suggestion of suggestions.filter((s) => !s.startsWith("Optional"))) {
-            console.log(chalk.gray(`     ${suggestion}`));
+        else if (warnings.length > 0) {
+            console.log(chalk.yellow("⚠️  Prerequisites:\n"));
+            for (const warning of warnings) {
+                console.log(chalk.yellow(`   • ${warning}`));
+            }
+            for (const suggestion of suggestions.filter((s) => !s.startsWith("Optional"))) {
+                console.log(chalk.gray(`     ${suggestion}`));
+            }
+            console.log();
         }
-        console.log();
     }
     // Check if already initialized
     const configExists = await fileExists(".claude/settings.json");
@@ -249,9 +277,10 @@ export async function initCommand(options) {
     const optionalSection = optionalSuggestions.length > 0
         ? `\n${chalk.bold("Optional improvements:")}\n${optionalSuggestions.map((s) => `  • ${s.replace("Optional: ", "")}`).join("\n")}\n`
         : "";
-    // Build prerequisites reminder if there were warnings
-    const prereqReminder = warnings.length > 0
-        ? `\n${chalk.yellow("⚠️  Remember to address prerequisites above before using issue workflows.")}\n`
+    // Build prerequisites reminder if there were remaining issues from wizard or warnings
+    const hasRemainingIssues = wizardRemainingIssues.length > 0 || warnings.length > 0;
+    const prereqReminder = hasRemainingIssues
+        ? `\n${chalk.yellow("⚠️  Remember to install missing dependencies before using issue workflows.")}\n${chalk.gray("   Run 'sequant doctor' to verify your setup.\n")}`
         : "";
     // Success message
     console.log(chalk.green(`