sequant 1.2.7 → 1.4.0

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
@@ -352,6 +354,7 @@ 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

@@ -1 +1 @@
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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 @@
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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/commands/init.ts"],"names":[],"mappings":"AAAA;;GAEG;AA4DH,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;AA2CD,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAqRrE"}

package/dist/src/commands/init.js

@@ -3,7 +3,7 @@
  */
 import chalk from "chalk";
 import inquirer from "inquirer";
-import { detectStack, getStackConfig, detectPackageManager, } from "../lib/stacks.js";
+import { detectStack, getStackConfig, detectPackageManager, getPackageManagerCommands, } from "../lib/stacks.js";
 import { copyTemplates } from "../lib/templates.js";
 import { createManifest } from "../lib/manifest.js";
 import { saveConfig } from "../lib/config.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
  */
@@ -77,17 +78,46 @@ 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(`     ${suggestion}`));
+            }
+            console.log();
         }
-        console.log();
     }
     // Check if already initialized
     const configExists = await fileExists(".claude/settings.json");
@@ -223,7 +253,13 @@ export async function initCommand(options) {
     }
     // Save config with tokens
     console.log(chalk.blue("💾 Saving configuration..."));
-    const tokens = { DEV_URL: devUrl };
+    const pmConfig = packageManager
+        ? getPackageManagerCommands(packageManager)
+        : getPackageManagerCommands("npm");
+    const tokens = {
+        DEV_URL: devUrl,
+        PM_RUN: pmConfig.run, // e.g., "npm run", "bun run", "yarn", "pnpm run"
+    };
     await saveConfig({
         tokens,
         stack: stack,
@@ -243,9 +279,10 @@ export async function initCommand(options) {
     const optionalSection = optionalSuggestions.length > 0
         ? `\n${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(`

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

@@ -1 +1 @@
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package/dist/src/commands/init.test.js

@@ -60,6 +60,22 @@ vi.mock("../lib/system.js", () => ({
 vi.mock("../lib/tty.js", () => ({
     shouldUseInteractiveMode: vi.fn(),
     getNonInteractiveReason: vi.fn(),
+    isCI: vi.fn(),
+}));
+// Mock wizard functions
+vi.mock("../lib/wizard.js", () => ({
+    checkAllDependencies: vi.fn(() => ({
+        dependencies: [],
+        allRequiredMet: true,
+        hasMissing: false,
+    })),
+    displayDependencyStatus: vi.fn(),
+    runSetupWizard: vi.fn(() => Promise.resolve({
+        skipped: false,
+        completed: true,
+        remainingIssues: [],
+    })),
+    shouldRunSetupWizard: vi.fn(() => false),
 }));
 // Mock inquirer
 vi.mock("inquirer", () => ({
@@ -122,24 +138,26 @@ describe("init command", () => {
             expect(output).not.toContain("GitHub CLI is not authenticated");
             expect(output).toContain("Sequant initialized successfully");
         });
-        it("warns when gh CLI is not installed", async () => {
+        it("warns when gh CLI is not installed (with --skip-setup)", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "gh");
             mockIsGhAuthenticated.mockReturnValue(false);
-            await initCommand({ yes: true, stack: "generic" });
+            // Using skipSetup triggers legacy warning behavior
+            await initCommand({ yes: true, stack: "generic", skipSetup: true });
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Prerequisites:");
             expect(output).toContain("GitHub CLI (gh) is not installed");
-            expect(output).toContain("Remember to address prerequisites");
+            expect(output).toContain("Remember to install missing dependencies");
         });
-        it("warns when gh CLI is not authenticated", async () => {
+        it("warns when gh CLI is not authenticated (with --skip-setup)", async () => {
             mockCommandExists.mockReturnValue(true);
             mockIsGhAuthenticated.mockReturnValue(false);
-            await initCommand({ yes: true, stack: "generic" });
+            // Using skipSetup triggers legacy warning behavior
+            await initCommand({ yes: true, stack: "generic", skipSetup: true });
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Prerequisites:");
             expect(output).toContain("GitHub CLI is not authenticated");
             expect(output).toContain("gh auth login");
-            expect(output).toContain("Remember to address prerequisites");
+            expect(output).toContain("Remember to install missing dependencies");
         });
         it("shows optional jq suggestion when jq is not installed", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "jq");
@@ -151,24 +169,31 @@ describe("init command", () => {
             // Should NOT show prerequisites warning since jq is optional
             expect(output).not.toContain("Prerequisites:");
         });
-        it("shows both gh warning and jq suggestion when both are missing", async () => {
+        it("shows both gh warning and jq suggestion when both are missing (with --skip-setup)", async () => {
             mockCommandExists.mockReturnValue(false);
             mockIsGhAuthenticated.mockReturnValue(false);
-            await initCommand({ yes: true, stack: "generic" });
+            // Using skipSetup triggers legacy warning behavior
+            await initCommand({ yes: true, stack: "generic", skipSetup: true });
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             expect(output).toContain("Prerequisites:");
             expect(output).toContain("GitHub CLI (gh) is not installed");
             expect(output).toContain("Optional improvements:");
             expect(output).toContain("Install jq for faster JSON parsing");
         });
-        it("skips auth check when gh is not installed", async () => {
+        it("skips auth check when gh is not installed (with --skip-setup)", async () => {
             mockCommandExists.mockImplementation((cmd) => cmd !== "gh");
-            await initCommand({ yes: true, stack: "generic" });
+            // Using skipSetup triggers legacy warning behavior
+            await initCommand({ yes: true, stack: "generic", skipSetup: true });
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
             // Should only show "not installed", not "not authenticated"
             expect(output).toContain("GitHub CLI (gh) is not installed");
             expect(output).not.toContain("GitHub CLI is not authenticated");
         });
+        it("shows skip-setup message when wizard is skipped", async () => {
+            await initCommand({ yes: true, stack: "generic", skipSetup: true });
+            const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");
+            expect(output).toContain("Skipping dependency setup wizard");
+        });
     });
     describe("initialization flow", () => {
         it("completes successfully with --yes and --stack flags", async () => {
@@ -183,11 +208,12 @@ describe("init command", () => {
             expect(mockEnsureDir).toHaveBeenCalledWith("scripts/dev");
             expect(mockCreateDefaultSettings).toHaveBeenCalled();
             expect(mockSaveConfig).toHaveBeenCalledWith(expect.objectContaining({
-                tokens: { DEV_URL: "http://localhost:3000" },
+                tokens: { DEV_URL: "http://localhost:3000", PM_RUN: "npm run" },
                 stack: "nextjs",
             }));
             expect(mockCopyTemplates).toHaveBeenCalledWith("nextjs", {
                 DEV_URL: "http://localhost:3000",
+                PM_RUN: "npm run",
             });
             expect(mockCreateManifest).toHaveBeenCalledWith("nextjs", "npm");
             const output = consoleLogSpy.mock.calls.map((c) => c[0]).join("\n");

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

@@ -1 +1 @@
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package/dist/src/commands/run.d.ts

@@ -4,6 +4,7 @@
  * Runs the Sequant workflow (/spec → /exec → /qa) for one or more issues
  * using the Claude Agent SDK for proper skill invocation.
  */
+import { Phase } from "../lib/workflow/types.js";
 /**
  * List all active worktrees with their branches
  */
@@ -16,6 +17,25 @@ export declare function listWorktrees(): Array<{
  * Get changed files in a worktree compared to main
  */
 export declare function getWorktreeChangedFiles(worktreePath: string): string[];
+/**
+ * Detect phases based on issue labels (like /solve logic)
+ */
+export declare function detectPhasesFromLabels(labels: string[]): {
+    phases: Phase[];
+    qualityLoop: boolean;
+};
+/**
+ * Parse recommended workflow from /spec output
+ *
+ * Looks for:
+ * ## Recommended Workflow
+ * **Phases:** exec → qa
+ * **Quality Loop:** enabled|disabled
+ */
+export declare function parseRecommendedWorkflow(output: string): {
+    phases: Phase[];
+    qualityLoop: boolean;
+} | null;
 interface RunOptions {
     phases?: string;
     sequential?: boolean;

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

@@ -1 +1 @@
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+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../../src/commands/run.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAgBH,OAAO,EACL,KAAK,EAMN,MAAM,0BAA0B,CAAC;AA2DlC;;GAEG;AACH,wBAAgB,aAAa,IAAI,KAAK,CAAC;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;CACtB,CAAC,CAgCD;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,EAAE,CAYtE;AAuND;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG;IACxD,MAAM,EAAE,KAAK,EAAE,CAAC;IAChB,WAAW,EAAE,OAAO,CAAC;CACtB,CAiDA;AAED;;;;;;;GAOG;AACH,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,MAAM,GAAG;IACxD,MAAM,EAAE,KAAK,EAAE,CAAC;IAChB,WAAW,EAAE,OAAO,CAAC;CACtB,GAAG,IAAI,CAgDP;AAED,UAAU,UAAU;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,6DAA6D;IAC7D,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,4DAA4D;IAC5D,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B;AA+bD;;GAEG;AACH,wBAAsB,UAAU,CAC9B,MAAM,EAAE,MAAM,EAAE,EAChB,OAAO,EAAE,UAAU,GAClB,OAAO,CAAC,IAAI,CAAC,CAoVf"}

package/dist/src/commands/run.js

@@ -219,6 +219,7 @@ async function ensureWorktrees(issues, verbose, packageManager) {
  */
 const PHASE_PROMPTS = {
     spec: "Review GitHub issue #{issue} and create an implementation plan with verification criteria. Run the /spec {issue} workflow.",
+    "security-review": "Perform a deep security analysis for GitHub issue #{issue} focusing on auth, permissions, and sensitive operations. Run the /security-review {issue} workflow.",
     testgen: "Generate test stubs for GitHub issue #{issue} based on the specification. Run the /testgen {issue} workflow.",
     exec: "Implement the feature for GitHub issue #{issue} following the spec. Run the /exec {issue} workflow.",
     test: "Execute structured browser-based testing for GitHub issue #{issue}. Run the /test {issue} workflow.",
@@ -241,10 +242,20 @@ const DOCS_LABELS = ["docs", "documentation", "readme"];
  * Complex labels that enable quality loop
  */
 const COMPLEX_LABELS = ["complex", "refactor", "breaking", "major"];
+/**
+ * Security-related labels that trigger security-review phase
+ */
+const SECURITY_LABELS = [
+    "security",
+    "auth",
+    "authentication",
+    "permissions",
+    "admin",
+];
 /**
  * Detect phases based on issue labels (like /solve logic)
  */
-function detectPhasesFromLabels(labels) {
+export function detectPhasesFromLabels(labels) {
     const lowerLabels = labels.map((l) => l.toLowerCase());
     // Check for bug/fix labels → exec → qa (skip spec)
     const isBugFix = lowerLabels.some((label) => BUG_LABELS.some((bugLabel) => label.includes(bugLabel)));
@@ -254,6 +265,8 @@ function detectPhasesFromLabels(labels) {
     const isUI = lowerLabels.some((label) => UI_LABELS.some((uiLabel) => label.includes(uiLabel)));
     // Check for complex labels → enable quality loop
     const isComplex = lowerLabels.some((label) => COMPLEX_LABELS.some((complexLabel) => label.includes(complexLabel)));
+    // Check for security labels → add security-review phase
+    const isSecurity = lowerLabels.some((label) => SECURITY_LABELS.some((secLabel) => label.includes(secLabel)));
     // Build phase list
     let phases;
     if (isBugFix || isDocs) {
@@ -268,6 +281,11 @@ function detectPhasesFromLabels(labels) {
         // Standard workflow: spec → exec → qa
         phases = ["spec", "exec", "qa"];
     }
+    // Add security-review phase after spec if security labels detected
+    if (isSecurity && phases.includes("spec")) {
+        const specIndex = phases.indexOf("spec");
+        phases.splice(specIndex + 1, 0, "security-review");
+    }
     return { phases, qualityLoop: isComplex };
 }
 /**
@@ -278,7 +296,7 @@ function detectPhasesFromLabels(labels) {
  * **Phases:** exec → qa
  * **Quality Loop:** enabled|disabled
  */
-function parseRecommendedWorkflow(output) {
+export function parseRecommendedWorkflow(output) {
     // Find the Recommended Workflow section
     const workflowMatch = output.match(/## Recommended Workflow[\s\S]*?\*\*Phases:\*\*\s*([^\n]+)/i);
     if (!workflowMatch) {
@@ -293,7 +311,15 @@ function parseRecommendedWorkflow(output) {
     // Validate and convert to Phase type
     const validPhases = [];
     for (const name of phaseNames) {
-        if (["spec", "testgen", "exec", "test", "qa", "loop"].includes(name)) {
+        if ([
+            "spec",
+            "security-review",
+            "testgen",
+            "exec",
+            "test",
+            "qa",
+            "loop",
+        ].includes(name)) {
             validPhases.push(name);
         }
     }
@@ -375,6 +401,10 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath)
             env.SEQUANT_WORKTREE = worktreePath;
             env.SEQUANT_ISSUE = String(issueNumber);
         }
+        // Set orchestration context for skills to detect they're part of a workflow
+        // Skills can check these to skip redundant pre-flight checks
+        env.SEQUANT_ORCHESTRATOR = "sequant-run";
+        env.SEQUANT_PHASE = phase;
         // Execute using Claude Agent SDK
         // Note: Don't resume sessions when switching to worktree (different cwd breaks resume)
         const canResume = sessionId && !shouldUseWorktree;