sequant 1.3.1 → 1.5.0

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 () => {

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

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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;AA4DlC;;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;AAodD;;GAEG;AACH,wBAAsB,UAAU,CAC9B,MAAM,EAAE,MAAM,EAAE,EAChB,OAAO,EAAE,UAAU,GAClB,OAAO,CAAC,IAAI,CAAC,CAiZf"}

package/dist/src/commands/run.js

@@ -14,6 +14,7 @@ import { getSettings } from "../lib/settings.js";
 import { PM_CONFIG } from "../lib/stacks.js";
 import { LogWriter, createPhaseLogFromTiming, } from "../lib/workflow/log-writer.js";
 import { DEFAULT_PHASES, DEFAULT_CONFIG, } from "../lib/workflow/types.js";
+import { ShutdownManager } from "../lib/shutdown.js";
 /**
  * Slugify a title for branch naming
  */
@@ -358,7 +359,7 @@ const ISOLATED_PHASES = ["exec", "test", "qa"];
 /**
  * Execute a single phase for an issue using Claude Agent SDK
  */
-async function executePhase(issueNumber, phase, config, sessionId, worktreePath) {
+async function executePhase(issueNumber, phase, config, sessionId, worktreePath, shutdownManager) {
     const startTime = Date.now();
     if (config.dryRun) {
         // Dry run - just simulate
@@ -382,11 +383,24 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath)
     const shouldUseWorktree = worktreePath && ISOLATED_PHASES.includes(phase);
     const cwd = shouldUseWorktree ? worktreePath : process.cwd();
     try {
+        // Check if shutdown is in progress
+        if (shutdownManager?.shuttingDown) {
+            return {
+                phase,
+                success: false,
+                durationSeconds: 0,
+                error: "Shutdown in progress",
+            };
+        }
         // Create abort controller for timeout
         const abortController = new AbortController();
         const timeoutId = setTimeout(() => {
             abortController.abort();
         }, config.phaseTimeout * 1000);
+        // Register abort controller with shutdown manager for graceful shutdown
+        if (shutdownManager) {
+            shutdownManager.setAbortController(abortController);
+        }
         let resultSessionId;
         let resultMessage;
         let lastError;
@@ -455,6 +469,10 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath)
             }
         }
         clearTimeout(timeoutId);
+        // Clear abort controller from shutdown manager
+        if (shutdownManager) {
+            shutdownManager.clearAbortController();
+        }
         const durationSeconds = (Date.now() - startTime) / 1000;
         // Check result status
         if (resultMessage) {
@@ -651,7 +669,7 @@ function hasUILabels(labels) {
  * Determine phases to run based on options and issue labels
  */
 function determinePhasesForIssue(basePhases, labels, options) {
-    let phases = [...basePhases];
+    const phases = [...basePhases];
     // Add testgen phase after spec if requested
     if (options.testgen && phases.includes("spec")) {
         const specIndex = phases.indexOf("spec");
@@ -797,6 +815,15 @@ export async function runCommand(issues, options) {
         });
         await logWriter.initialize(runConfig);
     }
+    // Initialize shutdown manager for graceful interruption handling
+    const shutdown = new ShutdownManager();
+    // Register log writer finalization as cleanup task
+    if (logWriter) {
+        const writer = logWriter; // Capture for closure
+        shutdown.registerCleanup("Finalize run logs", async () => {
+            await writer.finalize();
+        });
+    }
     // Display configuration
     console.log(chalk.gray(`  Stack: ${manifest.stack}`));
     if (autoDetectPhases) {
@@ -840,112 +867,149 @@ export async function runCommand(issues, options) {
             title: issueInfoMap.get(num)?.title || `Issue #${num}`,
         }));
         worktreeMap = await ensureWorktrees(issueData, config.verbose, manifest.packageManager);
-    }
-    // Execute
-    const results = [];
-    if (batches) {
-        // Batch execution: run batches sequentially, issues within batch based on mode
-        for (let batchIdx = 0; batchIdx < batches.length; batchIdx++) {
-            const batch = batches[batchIdx];
-            console.log(chalk.blue(`\n  Batch ${batchIdx + 1}/${batches.length}: Issues ${batch.map((n) => `#${n}`).join(", ")}`));
-            const batchResults = await executeBatch(batch, config, logWriter, mergedOptions, issueInfoMap, worktreeMap);
-            results.push(...batchResults);
-            // Check if batch failed and we should stop
-            const batchFailed = batchResults.some((r) => !r.success);
-            if (batchFailed && config.sequential) {
-                console.log(chalk.yellow(`\n  ⚠️  Batch ${batchIdx + 1} failed, stopping batch execution`));
-                break;
+        // Register cleanup tasks for newly created worktrees (not pre-existing ones)
+        for (const [issueNum, worktree] of worktreeMap.entries()) {
+            if (!worktree.existed) {
+                shutdown.registerCleanup(`Cleanup worktree for #${issueNum}`, async () => {
+                    // Remove worktree (leaves branch intact for recovery)
+                    const result = spawnSync("git", ["worktree", "remove", "--force", worktree.path], {
+                        stdio: "pipe",
+                    });
+                    if (result.status !== 0 && config.verbose) {
+                        console.log(chalk.yellow(`    Warning: Could not remove worktree ${worktree.path}`));
+                    }
+                });
             }
         }
     }
-    else if (config.sequential) {
-        // Sequential execution
-        for (const issueNumber of issueNumbers) {
-            const issueInfo = issueInfoMap.get(issueNumber) ?? {
-                title: `Issue #${issueNumber}`,
-                labels: [],
-            };
-            const worktreeInfo = worktreeMap.get(issueNumber);
-            // Start issue logging
-            if (logWriter) {
-                logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
-            }
-            const result = await runIssueWithLogging(issueNumber, config, logWriter, issueInfo.labels, mergedOptions, worktreeInfo?.path);
-            results.push(result);
-            // Complete issue logging
-            if (logWriter) {
-                logWriter.completeIssue();
-            }
-            if (!result.success) {
-                console.log(chalk.yellow(`\n  ⚠️  Issue #${issueNumber} failed, stopping sequential execution`));
-                break;
+    // Execute with graceful shutdown handling
+    const results = [];
+    let exitCode = 0;
+    try {
+        if (batches) {
+            // Batch execution: run batches sequentially, issues within batch based on mode
+            for (let batchIdx = 0; batchIdx < batches.length; batchIdx++) {
+                const batch = batches[batchIdx];
+                console.log(chalk.blue(`\n  Batch ${batchIdx + 1}/${batches.length}: Issues ${batch.map((n) => `#${n}`).join(", ")}`));
+                const batchResults = await executeBatch(batch, config, logWriter, mergedOptions, issueInfoMap, worktreeMap, shutdown);
+                results.push(...batchResults);
+                // Check if batch failed and we should stop
+                const batchFailed = batchResults.some((r) => !r.success);
+                if (batchFailed && config.sequential) {
+                    console.log(chalk.yellow(`\n  ⚠️  Batch ${batchIdx + 1} failed, stopping batch execution`));
+                    break;
+                }
             }
         }
-    }
-    else {
-        // Parallel execution (for now, just run sequentially but don't stop on failure)
-        // TODO: Add proper parallel execution with listr2
-        for (const issueNumber of issueNumbers) {
-            const issueInfo = issueInfoMap.get(issueNumber) ?? {
-                title: `Issue #${issueNumber}`,
-                labels: [],
-            };
-            const worktreeInfo = worktreeMap.get(issueNumber);
-            // Start issue logging
-            if (logWriter) {
-                logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
+        else if (config.sequential) {
+            // Sequential execution
+            for (const issueNumber of issueNumbers) {
+                const issueInfo = issueInfoMap.get(issueNumber) ?? {
+                    title: `Issue #${issueNumber}`,
+                    labels: [],
+                };
+                const worktreeInfo = worktreeMap.get(issueNumber);
+                // Start issue logging
+                if (logWriter) {
+                    logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
+                }
+                const result = await runIssueWithLogging(issueNumber, config, logWriter, issueInfo.labels, mergedOptions, worktreeInfo?.path, shutdown);
+                results.push(result);
+                // Complete issue logging
+                if (logWriter) {
+                    logWriter.completeIssue();
+                }
+                // Check if shutdown was triggered
+                if (shutdown.shuttingDown) {
+                    break;
+                }
+                if (!result.success) {
+                    console.log(chalk.yellow(`\n  ⚠️  Issue #${issueNumber} failed, stopping sequential execution`));
+                    break;
+                }
             }
-            const result = await runIssueWithLogging(issueNumber, config, logWriter, issueInfo.labels, mergedOptions, worktreeInfo?.path);
-            results.push(result);
-            // Complete issue logging
-            if (logWriter) {
-                logWriter.completeIssue();
+        }
+        else {
+            // Parallel execution (for now, just run sequentially but don't stop on failure)
+            // TODO: Add proper parallel execution with listr2
+            for (const issueNumber of issueNumbers) {
+                // Check if shutdown was triggered
+                if (shutdown.shuttingDown) {
+                    break;
+                }
+                const issueInfo = issueInfoMap.get(issueNumber) ?? {
+                    title: `Issue #${issueNumber}`,
+                    labels: [],
+                };
+                const worktreeInfo = worktreeMap.get(issueNumber);
+                // Start issue logging
+                if (logWriter) {
+                    logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
+                }
+                const result = await runIssueWithLogging(issueNumber, config, logWriter, issueInfo.labels, mergedOptions, worktreeInfo?.path, shutdown);
+                results.push(result);
+                // Complete issue logging
+                if (logWriter) {
+                    logWriter.completeIssue();
+                }
             }
         }
-    }
-    // Finalize log
-    let logPath = null;
-    if (logWriter) {
-        logPath = await logWriter.finalize();
-    }
-    // Summary
-    console.log(chalk.blue("\n" + "━".repeat(50)));
-    console.log(chalk.blue("  Summary"));
-    console.log(chalk.blue("━".repeat(50)));
-    const passed = results.filter((r) => r.success).length;
-    const failed = results.filter((r) => !r.success).length;
-    console.log(chalk.gray(`\n  Results: ${chalk.green(`${passed} passed`)}, ${chalk.red(`${failed} failed`)}`));
-    for (const result of results) {
-        const status = result.success ? chalk.green("✓") : chalk.red("✗");
-        const duration = result.durationSeconds
-            ? chalk.gray(` (${formatDuration(result.durationSeconds)})`)
-            : "";
-        const phases = result.phaseResults
-            .map((p) => (p.success ? chalk.green(p.phase) : chalk.red(p.phase)))
-            .join(" → ");
-        const loopInfo = result.loopTriggered ? chalk.yellow(" [loop]") : "";
-        console.log(`  ${status} #${result.issueNumber}: ${phases}${loopInfo}${duration}`);
-    }
-    console.log("");
-    if (logPath) {
-        console.log(chalk.gray(`  📝 Log: ${logPath}`));
+        // Finalize log
+        let logPath = null;
+        if (logWriter) {
+            logPath = await logWriter.finalize();
+        }
+        // Summary
+        console.log(chalk.blue("\n" + "━".repeat(50)));
+        console.log(chalk.blue("  Summary"));
+        console.log(chalk.blue("━".repeat(50)));
+        const passed = results.filter((r) => r.success).length;
+        const failed = results.filter((r) => !r.success).length;
+        console.log(chalk.gray(`\n  Results: ${chalk.green(`${passed} passed`)}, ${chalk.red(`${failed} failed`)}`));
+        for (const result of results) {
+            const status = result.success ? chalk.green("✓") : chalk.red("✗");
+            const duration = result.durationSeconds
+                ? chalk.gray(` (${formatDuration(result.durationSeconds)})`)
+                : "";
+            const phases = result.phaseResults
+                .map((p) => (p.success ? chalk.green(p.phase) : chalk.red(p.phase)))
+                .join(" → ");
+            const loopInfo = result.loopTriggered ? chalk.yellow(" [loop]") : "";
+            console.log(`  ${status} #${result.issueNumber}: ${phases}${loopInfo}${duration}`);
+        }
         console.log("");
+        if (logPath) {
+            console.log(chalk.gray(`  📝 Log: ${logPath}`));
+            console.log("");
+        }
+        if (config.dryRun) {
+            console.log(chalk.yellow("  ℹ️  This was a dry run. Use without --dry-run to execute."));
+            console.log("");
+        }
+        // Set exit code if any failed
+        if (failed > 0 && !config.dryRun) {
+            exitCode = 1;
+        }
     }
-    if (config.dryRun) {
-        console.log(chalk.yellow("  ℹ️  This was a dry run. Use without --dry-run to execute."));
-        console.log("");
+    finally {
+        // Always dispose shutdown manager to clean up signal handlers
+        shutdown.dispose();
     }
-    // Exit with error if any failed
-    if (failed > 0 && !config.dryRun) {
-        process.exit(1);
+    // Exit with error if any failed (outside try/finally so dispose() runs first)
+    if (exitCode !== 0) {
+        process.exit(exitCode);
     }
 }
 /**
  * Execute a batch of issues
  */
-async function executeBatch(issueNumbers, config, logWriter, options, issueInfoMap, worktreeMap) {
+async function executeBatch(issueNumbers, config, logWriter, options, issueInfoMap, worktreeMap, shutdownManager) {
     const results = [];
     for (const issueNumber of issueNumbers) {
+        // Check if shutdown was triggered
+        if (shutdownManager?.shuttingDown) {
+            break;
+        }
         const issueInfo = issueInfoMap.get(issueNumber) ?? {
             title: `Issue #${issueNumber}`,
             labels: [],
@@ -955,7 +1019,7 @@ async function executeBatch(issueNumbers, config, logWriter, options, issueInfoM
         if (logWriter) {
             logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
         }
-        const result = await runIssueWithLogging(issueNumber, config, logWriter, issueInfo.labels, options, worktreeInfo?.path);
+        const result = await runIssueWithLogging(issueNumber, config, logWriter, issueInfo.labels, options, worktreeInfo?.path, shutdownManager);
         results.push(result);
         // Complete issue logging
         if (logWriter) {
@@ -967,7 +1031,7 @@ async function executeBatch(issueNumbers, config, logWriter, options, issueInfoM
 /**
  * Execute all phases for a single issue with logging and quality loop
  */
-async function runIssueWithLogging(issueNumber, config, logWriter, labels, options, worktreePath) {
+async function runIssueWithLogging(issueNumber, config, logWriter, labels, options, worktreePath, shutdownManager) {
     const startTime = Date.now();
     const phaseResults = [];
     let loopTriggered = false;
@@ -995,7 +1059,8 @@ async function runIssueWithLogging(issueNumber, config, logWriter, labels, optio
             console.log(chalk.gray(`    ⏳ spec...`));
             const specStartTime = new Date();
             // Note: spec runs in main repo (not worktree) for planning
-            const specResult = await executePhase(issueNumber, "spec", config, sessionId, worktreePath);
+            const specResult = await executePhase(issueNumber, "spec", config, sessionId, worktreePath, // Will be ignored for spec (non-isolated phase)
+            shutdownManager);
             const specEndTime = new Date();
             if (specResult.sessionId) {
                 sessionId = specResult.sessionId;
@@ -1027,7 +1092,7 @@ async function runIssueWithLogging(issueNumber, config, logWriter, labels, optio
                 : "";
             console.log(chalk.green(`    ✓ spec${duration}`));
             // Parse recommended workflow from spec output
-            let parsedWorkflow = specResult.output
+            const parsedWorkflow = specResult.output
                 ? parseRecommendedWorkflow(specResult.output)
                 : null;
             if (parsedWorkflow) {
@@ -1082,7 +1147,7 @@ async function runIssueWithLogging(issueNumber, config, logWriter, labels, optio
         for (const phase of phases) {
             console.log(chalk.gray(`    ⏳ ${phase}...`));
             const phaseStartTime = new Date();
-            const result = await executePhase(issueNumber, phase, config, sessionId, worktreePath);
+            const result = await executePhase(issueNumber, phase, config, sessionId, worktreePath, shutdownManager);
             const phaseEndTime = new Date();
             // Capture session ID for subsequent phases
             if (result.sessionId) {
@@ -1110,7 +1175,7 @@ async function runIssueWithLogging(issueNumber, config, logWriter, labels, optio
                 // If quality loop enabled, run loop phase to fix issues
                 if (useQualityLoop && iteration < maxIterations) {
                     console.log(chalk.yellow(`    Running /loop to fix issues...`));
-                    const loopResult = await executePhase(issueNumber, "loop", config, sessionId, worktreePath);
+                    const loopResult = await executePhase(issueNumber, "loop", config, sessionId, worktreePath, shutdownManager);
                     phaseResults.push(loopResult);
                     if (loopResult.sessionId) {
                         sessionId = loopResult.sessionId;