sequant 1.17.0 → 1.18.0

package/dist/src/commands/run.js

@@ -1,1557 +1,37 @@
 /**
  * sequant run - Execute workflow for GitHub issues
  *
- * Runs the Sequant workflow (/spec → /exec → /qa) for one or more issues
- * using the Claude Agent SDK for proper skill invocation.
+ * Orchestrator module that composes focused workflow modules:
+ * - worktree-manager: Worktree lifecycle (ensure, list, cleanup, changed files)
+ * - phase-executor: Phase execution with retry and failure handling
+ * - phase-mapper: Label-to-phase detection and workflow parsing
+ * - batch-executor: Batch execution, dependency sorting, issue logging
  */
 import chalk from "chalk";
 import { spawnSync } from "child_process";
-import { existsSync, readFileSync } from "fs";
-import path from "path";
-import { query } from "@anthropic-ai/claude-agent-sdk";
 import { getManifest } from "../lib/manifest.js";
 import { getSettings } from "../lib/settings.js";
-import { PM_CONFIG } from "../lib/stacks.js";
-import { LogWriter, createPhaseLogFromTiming, } from "../lib/workflow/log-writer.js";
+import { LogWriter } from "../lib/workflow/log-writer.js";
 import { StateManager } from "../lib/workflow/state-manager.js";
 import { DEFAULT_PHASES, DEFAULT_CONFIG, } from "../lib/workflow/types.js";
 import { ShutdownManager } from "../lib/shutdown.js";
-import { getMcpServersConfig } from "../lib/system.js";
 import { checkVersionCached, getVersionWarning } from "../lib/version-check.js";
 import { MetricsWriter } from "../lib/workflow/metrics-writer.js";
 import { determineOutcome, } from "../lib/workflow/metrics-schema.js";
-import { getResumablePhasesForIssue } from "../lib/workflow/phase-detection.js";
 import { ui, colors } from "../lib/cli-ui.js";
-import { PhaseSpinner } from "../lib/phase-spinner.js";
-import { getGitDiffStats, getCommitHash, } from "../lib/workflow/git-diff-utils.js";
+import { getCommitHash } from "../lib/workflow/git-diff-utils.js";
 import { getTokenUsageForRun } from "../lib/workflow/token-utils.js";
 import { reconcileStateAtStartup } from "../lib/workflow/state-utils.js";
 import { analyzeRun, formatReflection } from "../lib/workflow/run-reflect.js";
-/**
- * Slugify a title for branch naming
- */
-function slugify(title) {
-    return title
-        .toLowerCase()
-        .replace(/[^a-z0-9]+/g, "-")
-        .replace(/^-+|-+$/g, "")
-        .substring(0, 50);
-}
-/**
- * Parse QA verdict from phase output
- *
- * Looks for verdict patterns in the QA output:
- * - "### Verdict: READY_FOR_MERGE"
- * - "**Verdict:** AC_NOT_MET"
- * - "Verdict: AC_MET_BUT_NOT_A_PLUS"
- *
- * @param output - The captured output from QA phase
- * @returns The parsed verdict or null if not found
- */
-export function parseQaVerdict(output) {
-    if (!output)
-        return null;
-    // Match various verdict formats:
-    // - "### Verdict: X" (markdown header)
-    // - "**Verdict:** X" (bold label with colon inside)
-    // - "**Verdict:** **X**" (bold label and bold value)
-    // - "Verdict: X" (plain)
-    // Case insensitive, handles optional markdown formatting
-    const verdictMatch = output.match(/(?:###?\s*)?(?:\*\*)?Verdict:?\*?\*?\s*\*?\*?\s*(READY_FOR_MERGE|AC_MET_BUT_NOT_A_PLUS|AC_NOT_MET|NEEDS_VERIFICATION)\*?\*?/i);
-    if (!verdictMatch)
-        return null;
-    // Normalize to uppercase with underscores
-    const verdict = verdictMatch[1].toUpperCase().replace(/-/g, "_");
-    return verdict;
-}
-/**
- * Get the git repository root directory
- */
-function getGitRoot() {
-    const result = spawnSync("git", ["rev-parse", "--show-toplevel"], {
-        stdio: "pipe",
-    });
-    if (result.status === 0) {
-        return result.stdout.toString().trim();
-    }
-    return null;
-}
-/**
- * Check if a worktree exists for a given branch
- */
-function findExistingWorktree(branch) {
-    const result = spawnSync("git", ["worktree", "list", "--porcelain"], {
-        stdio: "pipe",
-    });
-    if (result.status !== 0)
-        return null;
-    const output = result.stdout.toString();
-    const lines = output.split("\n");
-    let currentPath = "";
-    for (const line of lines) {
-        if (line.startsWith("worktree ")) {
-            currentPath = line.substring(9);
-        }
-        else if (line.startsWith("branch refs/heads/") && line.includes(branch)) {
-            return currentPath;
-        }
-    }
-    return null;
-}
-/**
- * Check if a worktree is stale (behind origin/main) and should be recreated
- *
- * @param worktreePath - Path to the worktree
- * @param verbose - Enable verbose output
- * @returns Freshness check result
- */
-export function checkWorktreeFreshness(worktreePath, verbose) {
-    const result = {
-        isStale: false,
-        commitsBehind: 0,
-        hasUncommittedChanges: false,
-        hasUnpushedCommits: false,
-    };
-    // Fetch latest main to ensure accurate comparison
-    spawnSync("git", ["-C", worktreePath, "fetch", "origin", "main"], {
-        stdio: "pipe",
-        timeout: 30000,
-    });
-    // Check for uncommitted changes
-    const statusResult = spawnSync("git", ["-C", worktreePath, "status", "--porcelain"], { stdio: "pipe" });
-    if (statusResult.status === 0) {
-        result.hasUncommittedChanges =
-            statusResult.stdout.toString().trim().length > 0;
-    }
-    // Get merge base with origin/main
-    const mergeBaseResult = spawnSync("git", ["-C", worktreePath, "merge-base", "HEAD", "origin/main"], { stdio: "pipe" });
-    if (mergeBaseResult.status !== 0) {
-        // Can't determine merge base - not stale
-        return result;
-    }
-    const mergeBase = mergeBaseResult.stdout.toString().trim();
-    // Get origin/main HEAD
-    const mainHeadResult = spawnSync("git", ["-C", worktreePath, "rev-parse", "origin/main"], { stdio: "pipe" });
-    if (mainHeadResult.status !== 0) {
-        return result;
-    }
-    const mainHead = mainHeadResult.stdout.toString().trim();
-    // Count commits behind main
-    if (mergeBase !== mainHead) {
-        const countResult = spawnSync("git", ["-C", worktreePath, "rev-list", "--count", `${mergeBase}..${mainHead}`], { stdio: "pipe" });
-        if (countResult.status === 0) {
-            result.commitsBehind = parseInt(countResult.stdout.toString().trim(), 10);
-            // Consider stale if more than 5 commits behind (configurable threshold)
-            result.isStale = result.commitsBehind > 5;
-        }
-    }
-    // Check for unpushed commits (work in progress)
-    const unpushedResult = spawnSync("git", ["-C", worktreePath, "log", "--oneline", "@{u}..HEAD"], { stdio: "pipe" });
-    if (unpushedResult.status === 0) {
-        result.hasUnpushedCommits =
-            unpushedResult.stdout.toString().trim().length > 0;
-    }
-    if (verbose && result.isStale) {
-        console.log(chalk.gray(`    📊 Worktree is ${result.commitsBehind} commits behind origin/main`));
-    }
-    return result;
-}
-/**
- * Remove and recreate a stale worktree
- *
- * @param existingPath - Path to existing worktree
- * @param branch - Branch name
- * @param verbose - Enable verbose output
- * @returns true if worktree was removed
- */
-export function removeStaleWorktree(existingPath, branch, verbose) {
-    if (verbose) {
-        console.log(chalk.gray(`    🗑️  Removing stale worktree...`));
-    }
-    // Remove the worktree
-    const removeResult = spawnSync("git", ["worktree", "remove", "--force", existingPath], { stdio: "pipe" });
-    if (removeResult.status !== 0) {
-        const error = removeResult.stderr.toString();
-        console.log(chalk.yellow(`    ⚠️  Could not remove worktree: ${error}`));
-        return false;
-    }
-    // Delete the branch so it can be recreated fresh
-    const deleteResult = spawnSync("git", ["branch", "-D", branch], {
-        stdio: "pipe",
-    });
-    if (deleteResult.status !== 0 && verbose) {
-        console.log(chalk.gray(`    ℹ️  Branch ${branch} not deleted (may not exist locally)`));
-    }
-    return true;
-}
-/**
- * List all active worktrees with their branches
- */
-export function listWorktrees() {
-    const result = spawnSync("git", ["worktree", "list", "--porcelain"], {
-        stdio: "pipe",
-    });
-    if (result.status !== 0)
-        return [];
-    const output = result.stdout.toString();
-    const lines = output.split("\n");
-    const worktrees = [];
-    let currentPath = "";
-    let currentBranch = "";
-    for (const line of lines) {
-        if (line.startsWith("worktree ")) {
-            currentPath = line.substring(9);
-        }
-        else if (line.startsWith("branch refs/heads/")) {
-            currentBranch = line.substring(18);
-            // Extract issue number from branch name (e.g., feature/123-some-title)
-            const issueMatch = currentBranch.match(/feature\/(\d+)-/);
-            const issue = issueMatch ? parseInt(issueMatch[1], 10) : null;
-            worktrees.push({ path: currentPath, branch: currentBranch, issue });
-            currentPath = "";
-            currentBranch = "";
-        }
-    }
-    return worktrees;
-}
-/**
- * Get changed files in a worktree compared to main
- */
-export function getWorktreeChangedFiles(worktreePath) {
-    const result = spawnSync("git", ["-C", worktreePath, "diff", "--name-only", "main...HEAD"], { stdio: "pipe" });
-    if (result.status !== 0)
-        return [];
-    return result.stdout
-        .toString()
-        .trim()
-        .split("\n")
-        .filter((f) => f.length > 0);
-}
-/**
- * Get diff stats for a worktree (files changed, lines added)
- * Returns aggregate metrics only - no file paths to preserve privacy
- */
-export function getWorktreeDiffStats(worktreePath) {
-    const result = spawnSync("git", ["-C", worktreePath, "diff", "--stat", "main...HEAD"], { stdio: "pipe" });
-    if (result.status !== 0) {
-        return { filesChanged: 0, linesAdded: 0 };
-    }
-    const output = result.stdout.toString();
-    const lines = output.trim().split("\n");
-    // Summary line is last and looks like: " 5 files changed, 100 insertions(+), 20 deletions(-)"
-    const summaryLine = lines[lines.length - 1];
-    if (!summaryLine) {
-        return { filesChanged: 0, linesAdded: 0 };
-    }
-    const filesMatch = summaryLine.match(/(\d+)\s+files?\s+changed/);
-    const insertionsMatch = summaryLine.match(/(\d+)\s+insertions?\(\+\)/);
-    return {
-        filesChanged: filesMatch ? parseInt(filesMatch[1], 10) : 0,
-        linesAdded: insertionsMatch ? parseInt(insertionsMatch[1], 10) : 0,
-    };
-}
-/**
- * Read cache metrics from QA phase (AC-7)
- *
- * @param worktreePath - Path to the worktree
- * @returns CacheMetrics or undefined if not available
- */
-function readCacheMetrics(worktreePath) {
-    const cacheMetricsPath = worktreePath
-        ? path.join(worktreePath, ".sequant/.cache/qa/cache-metrics.json")
-        : ".sequant/.cache/qa/cache-metrics.json";
-    if (!existsSync(cacheMetricsPath)) {
-        return undefined;
-    }
-    try {
-        const content = readFileSync(cacheMetricsPath, "utf-8");
-        const data = JSON.parse(content);
-        if (typeof data.hits === "number" &&
-            typeof data.misses === "number" &&
-            typeof data.skipped === "number") {
-            return {
-                hits: data.hits,
-                misses: data.misses,
-                skipped: data.skipped,
-            };
-        }
-    }
-    catch {
-        // Ignore parse errors
-    }
-    return undefined;
-}
-/**
- * Filter phases based on resume status.
- *
- * When `resume` is true, calls `getResumablePhasesForIssue` to determine
- * which phases have already completed (via GitHub issue comment markers)
- * and removes them from the execution list.
- *
- * @param issueNumber - GitHub issue number
- * @param phases - The phases to potentially filter
- * @param resume - Whether the --resume flag is set
- * @returns Object with filtered phases and any skipped phases
- */
-export function filterResumedPhases(issueNumber, phases, resume) {
-    if (!resume) {
-        return { phases: [...phases], skipped: [] };
-    }
-    const resumable = getResumablePhasesForIssue(issueNumber, phases);
-    const skipped = phases.filter((p) => !resumable.includes(p));
-    return { phases: resumable, skipped };
-}
-/**
- * Create or reuse a worktree for an issue
- * @param baseBranch - Optional branch to use as base instead of origin/main (for chain mode)
- * @param chainMode - If true and branch exists, rebase onto baseBranch instead of using as-is
- */
-async function ensureWorktree(issueNumber, title, verbose, packageManager, baseBranch, chainMode) {
-    const gitRoot = getGitRoot();
-    if (!gitRoot) {
-        console.log(chalk.red("    ❌ Not in a git repository"));
-        return null;
-    }
-    const slug = slugify(title);
-    const branch = `feature/${issueNumber}-${slug}`;
-    const worktreesDir = path.join(path.dirname(gitRoot), "worktrees");
-    const worktreePath = path.join(worktreesDir, branch);
-    // Check if worktree already exists
-    let existingPath = findExistingWorktree(branch);
-    if (existingPath) {
-        // AC-3: Check if worktree is stale and needs recreation
-        const freshness = checkWorktreeFreshness(existingPath, verbose);
-        if (freshness.isStale) {
-            // AC-3: Handle stale worktrees - check for work in progress
-            if (freshness.hasUncommittedChanges) {
-                console.log(chalk.yellow(`    ⚠️  Worktree is ${freshness.commitsBehind} commits behind main but has uncommitted changes`));
-                console.log(chalk.yellow(`    ℹ️  Keeping existing worktree. Commit or stash changes, then re-run.`));
-                // Continue with existing worktree
-            }
-            else if (freshness.hasUnpushedCommits) {
-                console.log(chalk.yellow(`    ⚠️  Worktree is ${freshness.commitsBehind} commits behind main but has unpushed commits`));
-                console.log(chalk.yellow(`    ℹ️  Keeping existing worktree with WIP commits.`));
-                // Continue with existing worktree
-            }
-            else {
-                // Safe to recreate - no uncommitted/unpushed work
-                console.log(chalk.yellow(`    ⚠️  Worktree is ${freshness.commitsBehind} commits behind main — recreating fresh`));
-                if (removeStaleWorktree(existingPath, branch, verbose)) {
-                    existingPath = null; // Will fall through to create new worktree
-                }
-            }
-        }
-    }
-    if (existingPath) {
-        if (verbose) {
-            console.log(chalk.gray(`    📂 Reusing existing worktree: ${existingPath}`));
-        }
-        // In chain mode, rebase existing worktree onto previous chain link
-        if (chainMode && baseBranch) {
-            if (verbose) {
-                console.log(chalk.gray(`    🔄 Rebasing existing worktree onto chain base (${baseBranch})...`));
-            }
-            const rebaseResult = spawnSync("git", ["-C", existingPath, "rebase", baseBranch], { stdio: "pipe" });
-            if (rebaseResult.status !== 0) {
-                const rebaseError = rebaseResult.stderr.toString();
-                // Check if it's a conflict
-                if (rebaseError.includes("CONFLICT") ||
-                    rebaseError.includes("could not apply")) {
-                    console.log(chalk.yellow(`    ⚠️  Rebase conflict detected. Aborting rebase and keeping original branch state.`));
-                    console.log(chalk.yellow(`    ℹ️  Branch ${branch} is not properly chained. Manual rebase may be required.`));
-                    // Abort the rebase to restore branch state
-                    spawnSync("git", ["-C", existingPath, "rebase", "--abort"], {
-                        stdio: "pipe",
-                    });
-                }
-                else {
-                    console.log(chalk.yellow(`    ⚠️  Rebase failed: ${rebaseError.trim()}`));
-                    console.log(chalk.yellow(`    ℹ️  Continuing with branch in its original state.`));
-                }
-                return {
-                    issue: issueNumber,
-                    path: existingPath,
-                    branch,
-                    existed: true,
-                    rebased: false,
-                };
-            }
-            if (verbose) {
-                console.log(chalk.green(`    ✅ Existing worktree rebased onto ${baseBranch}`));
-            }
-            return {
-                issue: issueNumber,
-                path: existingPath,
-                branch,
-                existed: true,
-                rebased: true,
-            };
-        }
-        return {
-            issue: issueNumber,
-            path: existingPath,
-            branch,
-            existed: true,
-            rebased: false,
-        };
-    }
-    // Check if branch exists (but no worktree)
-    const branchCheck = spawnSync("git", ["show-ref", "--verify", "--quiet", `refs/heads/${branch}`], { stdio: "pipe" });
-    const branchExists = branchCheck.status === 0;
-    if (verbose) {
-        console.log(chalk.gray(`    🌿 Creating worktree for #${issueNumber}...`));
-    }
-    // Determine the base for the new branch
-    // For custom base branches, use origin/<branch> if it's a remote-style reference
-    // For local branches (chain mode), use as-is
-    const isLocalBranch = baseBranch && !baseBranch.startsWith("origin/") && baseBranch !== "main";
-    const baseRef = baseBranch
-        ? isLocalBranch
-            ? baseBranch
-            : baseBranch.startsWith("origin/")
-                ? baseBranch
-                : `origin/${baseBranch}`
-        : "origin/main";
-    // Fetch the base branch to ensure worktree starts from fresh baseline
-    const branchToFetch = baseBranch
-        ? baseBranch.replace(/^origin\//, "")
-        : "main";
-    if (!isLocalBranch) {
-        if (verbose) {
-            console.log(chalk.gray(`    🔄 Fetching latest ${branchToFetch}...`));
-        }
-        const fetchResult = spawnSync("git", ["fetch", "origin", branchToFetch], {
-            stdio: "pipe",
-        });
-        if (fetchResult.status !== 0 && verbose) {
-            console.log(chalk.yellow(`    ⚠️  Could not fetch origin/${branchToFetch}, using local state`));
-        }
-    }
-    else if (verbose) {
-        console.log(chalk.gray(`    🔗 Chaining from branch: ${baseBranch}`));
-    }
-    // Ensure worktrees directory exists
-    if (!existsSync(worktreesDir)) {
-        spawnSync("mkdir", ["-p", worktreesDir], { stdio: "pipe" });
-    }
-    // Create the worktree
-    let createResult;
-    let needsRebase = false;
-    if (branchExists) {
-        // Use existing branch
-        createResult = spawnSync("git", ["worktree", "add", worktreePath, branch], {
-            stdio: "pipe",
-        });
-        // In chain mode with existing branch, mark for rebase onto previous chain link
-        if (chainMode && baseBranch) {
-            needsRebase = true;
-        }
-    }
-    else {
-        // Create new branch from base reference (origin/main or previous branch in chain)
-        createResult = spawnSync("git", ["worktree", "add", worktreePath, "-b", branch, baseRef], { stdio: "pipe" });
-    }
-    if (createResult.status !== 0) {
-        const error = createResult.stderr.toString();
-        console.log(chalk.red(`    ❌ Failed to create worktree: ${error}`));
-        return null;
-    }
-    // Rebase existing branch onto chain base if needed
-    let rebased = false;
-    if (needsRebase) {
-        if (verbose) {
-            console.log(chalk.gray(`    🔄 Rebasing existing branch onto previous chain link (${baseRef})...`));
-        }
-        const rebaseResult = spawnSync("git", ["-C", worktreePath, "rebase", baseRef], {
-            stdio: "pipe",
-        });
-        if (rebaseResult.status !== 0) {
-            const rebaseError = rebaseResult.stderr.toString();
-            // Check if it's a conflict
-            if (rebaseError.includes("CONFLICT") ||
-                rebaseError.includes("could not apply")) {
-                console.log(chalk.yellow(`    ⚠️  Rebase conflict detected. Aborting rebase and keeping original branch state.`));
-                console.log(chalk.yellow(`    ℹ️  Branch ${branch} is not properly chained. Manual rebase may be required.`));
-                // Abort the rebase to restore branch state
-                spawnSync("git", ["-C", worktreePath, "rebase", "--abort"], {
-                    stdio: "pipe",
-                });
-            }
-            else {
-                console.log(chalk.yellow(`    ⚠️  Rebase failed: ${rebaseError.trim()}`));
-                console.log(chalk.yellow(`    ℹ️  Continuing with branch in its original state.`));
-            }
-        }
-        else {
-            rebased = true;
-            if (verbose) {
-                console.log(chalk.green(`    ✅ Branch rebased onto ${baseRef}`));
-            }
-        }
-    }
-    // Copy .env.local if it exists
-    const envLocalSrc = path.join(gitRoot, ".env.local");
-    const envLocalDst = path.join(worktreePath, ".env.local");
-    if (existsSync(envLocalSrc) && !existsSync(envLocalDst)) {
-        spawnSync("cp", [envLocalSrc, envLocalDst], { stdio: "pipe" });
-    }
-    // Copy .claude/settings.local.json if it exists
-    const claudeSettingsSrc = path.join(gitRoot, ".claude", "settings.local.json");
-    const claudeSettingsDst = path.join(worktreePath, ".claude", "settings.local.json");
-    if (existsSync(claudeSettingsSrc) && !existsSync(claudeSettingsDst)) {
-        spawnSync("mkdir", ["-p", path.join(worktreePath, ".claude")], {
-            stdio: "pipe",
-        });
-        spawnSync("cp", [claudeSettingsSrc, claudeSettingsDst], { stdio: "pipe" });
-    }
-    // Install dependencies if needed
-    const nodeModulesPath = path.join(worktreePath, "node_modules");
-    if (!existsSync(nodeModulesPath)) {
-        if (verbose) {
-            console.log(chalk.gray(`    📦 Installing dependencies...`));
-        }
-        // Use detected package manager or default to npm
-        const pm = packageManager || "npm";
-        const pmConfig = PM_CONFIG[pm];
-        const [cmd, ...args] = pmConfig.installSilent.split(" ");
-        spawnSync(cmd, args, {
-            cwd: worktreePath,
-            stdio: "pipe",
-        });
-    }
-    if (verbose) {
-        console.log(chalk.green(`    ✅ Worktree ready: ${worktreePath}`));
-    }
-    return {
-        issue: issueNumber,
-        path: worktreePath,
-        branch,
-        existed: false,
-        rebased,
-    };
-}
-/**
- * Ensure worktrees exist for all issues before execution
- * @param baseBranch - Optional base branch for worktree creation (default: main)
- */
-async function ensureWorktrees(issues, verbose, packageManager, baseBranch) {
-    const worktrees = new Map();
-    const baseDisplay = baseBranch || "main";
-    console.log(chalk.blue(`\n  📂 Preparing worktrees from ${baseDisplay}...`));
-    for (const issue of issues) {
-        const worktree = await ensureWorktree(issue.number, issue.title, verbose, packageManager, baseBranch, false);
-        if (worktree) {
-            worktrees.set(issue.number, worktree);
-        }
-    }
-    const created = Array.from(worktrees.values()).filter((w) => !w.existed).length;
-    const reused = Array.from(worktrees.values()).filter((w) => w.existed).length;
-    if (created > 0 || reused > 0) {
-        console.log(chalk.gray(`  Worktrees: ${created} created, ${reused} reused`));
-    }
-    return worktrees;
-}
-/**
- * Ensure worktrees exist for all issues in chain mode
- * Each issue branches from the previous issue's branch
- * @param baseBranch - Optional starting base branch for the chain (default: main)
- */
-async function ensureWorktreesChain(issues, verbose, packageManager, baseBranch) {
-    const worktrees = new Map();
-    const baseDisplay = baseBranch || "main";
-    console.log(chalk.blue(`\n  🔗 Preparing chained worktrees from ${baseDisplay}...`));
-    // First issue starts from the specified base branch (or main)
-    let previousBranch = baseBranch;
-    for (const issue of issues) {
-        const worktree = await ensureWorktree(issue.number, issue.title, verbose, packageManager, previousBranch, // Chain from previous branch (or base branch for first issue)
-        true);
-        if (worktree) {
-            worktrees.set(issue.number, worktree);
-            previousBranch = worktree.branch; // Next issue will branch from this
-        }
-        else {
-            // If worktree creation fails, stop the chain
-            console.log(chalk.red(`  ❌ Chain broken: could not create worktree for #${issue.number}`));
-            break;
-        }
-    }
-    const created = Array.from(worktrees.values()).filter((w) => !w.existed).length;
-    const reused = Array.from(worktrees.values()).filter((w) => w.existed).length;
-    const rebased = Array.from(worktrees.values()).filter((w) => w.rebased).length;
-    if (created > 0 || reused > 0) {
-        let msg = `  Chained worktrees: ${created} created, ${reused} reused`;
-        if (rebased > 0) {
-            msg += `, ${rebased} rebased`;
-        }
-        console.log(chalk.gray(msg));
-    }
-    // Show chain structure
-    if (worktrees.size > 0) {
-        const chainOrder = issues
-            .filter((i) => worktrees.has(i.number))
-            .map((i) => `#${i.number}`)
-            .join(" → ");
-        console.log(chalk.gray(`  Chain: ${baseDisplay} → ${chainOrder}`));
-    }
-    return worktrees;
-}
-/**
- * Create a checkpoint commit in the worktree after QA passes
- * This allows recovery in case later issues in the chain fail
- * @internal Exported for testing
- */
-export function createCheckpointCommit(worktreePath, issueNumber, verbose) {
-    // Check if there are uncommitted changes
-    const statusResult = spawnSync("git", ["-C", worktreePath, "status", "--porcelain"], { stdio: "pipe" });
-    if (statusResult.status !== 0) {
-        if (verbose) {
-            console.log(chalk.yellow(`    ⚠️  Could not check git status for checkpoint`));
-        }
-        return false;
-    }
-    const hasChanges = statusResult.stdout.toString().trim().length > 0;
-    if (!hasChanges) {
-        if (verbose) {
-            console.log(chalk.gray(`    📌 No changes to checkpoint (already committed)`));
-        }
-        return true;
-    }
-    // Stage all changes
-    const addResult = spawnSync("git", ["-C", worktreePath, "add", "-A"], {
-        stdio: "pipe",
-    });
-    if (addResult.status !== 0) {
-        if (verbose) {
-            console.log(chalk.yellow(`    ⚠️  Could not stage changes for checkpoint`));
-        }
-        return false;
-    }
-    // Create checkpoint commit
-    const commitMessage = `checkpoint(#${issueNumber}): QA passed
-
-This is an automatic checkpoint commit created after issue #${issueNumber}
-passed QA in chain mode. It serves as a recovery point if later issues fail.`;
-    const commitResult = spawnSync("git", ["-C", worktreePath, "commit", "-m", commitMessage], { stdio: "pipe" });
-    if (commitResult.status !== 0) {
-        const error = commitResult.stderr.toString();
-        if (verbose) {
-            console.log(chalk.yellow(`    ⚠️  Could not create checkpoint commit: ${error}`));
-        }
-        return false;
-    }
-    console.log(chalk.green(`    📌 Checkpoint commit created for #${issueNumber}`));
-    return true;
-}
-/**
- * Lockfile names for different package managers
- */
-const LOCKFILES = [
-    "package-lock.json",
-    "pnpm-lock.yaml",
-    "bun.lock",
-    "yarn.lock",
-];
-/**
- * Check if any lockfile changed during a rebase and re-run install if needed.
- * This prevents dependency drift when the lockfile was updated on main.
- * @param worktreePath Path to the worktree
- * @param packageManager Package manager to use for install
- * @param verbose Whether to show verbose output
- * @param preRebaseRef Git ref pointing to pre-rebase HEAD (defaults to ORIG_HEAD,
- *        which git sets automatically after rebase). Using ORIG_HEAD captures all
- *        lockfile changes across multi-commit rebases, unlike HEAD~1 which only
- *        checks the last commit.
- * @returns true if reinstall was performed, false otherwise
- * @internal Exported for testing
- */
-export function reinstallIfLockfileChanged(worktreePath, packageManager, verbose, preRebaseRef = "ORIG_HEAD") {
-    // Compare pre-rebase state to current HEAD to detect all lockfile changes
-    // introduced by the rebase (including changes from main that were pulled in)
-    let lockfileChanged = false;
-    for (const lockfile of LOCKFILES) {
-        const result = spawnSync("git", [
-            "-C",
-            worktreePath,
-            "diff",
-            "--name-only",
-            `${preRebaseRef}..HEAD`,
-            "--",
-            lockfile,
-        ], { stdio: "pipe" });
-        if (result.status === 0 && result.stdout.toString().trim().length > 0) {
-            lockfileChanged = true;
-            if (verbose) {
-                console.log(chalk.gray(`    📦 Lockfile changed: ${lockfile}`));
-            }
-            break;
-        }
-    }
-    if (!lockfileChanged) {
-        if (verbose) {
-            console.log(chalk.gray(`    📦 No lockfile changes detected`));
-        }
-        return false;
-    }
-    // Re-run install to sync node_modules with updated lockfile
-    console.log(chalk.blue(`    📦 Reinstalling dependencies (lockfile changed)...`));
-    const pm = packageManager || "npm";
-    const pmConfig = PM_CONFIG[pm];
-    const [cmd, ...args] = pmConfig.installSilent.split(" ");
-    const installResult = spawnSync(cmd, args, {
-        cwd: worktreePath,
-        stdio: "pipe",
-    });
-    if (installResult.status !== 0) {
-        const error = installResult.stderr.toString();
-        console.log(chalk.yellow(`    ⚠️  Dependency reinstall failed: ${error.trim()}`));
-        return false;
-    }
-    console.log(chalk.green(`    ✅ Dependencies reinstalled`));
-    return true;
-}
-/**
- * Rebase the worktree branch onto origin/main before PR creation.
- * This ensures the branch is up-to-date and prevents lockfile drift.
- *
- * @param worktreePath Path to the worktree
- * @param issueNumber Issue number (for logging)
- * @param packageManager Package manager to use if reinstall needed
- * @param verbose Whether to show verbose output
- * @returns RebaseResult indicating success/failure and whether reinstall was performed
- * @internal Exported for testing
- */
-export function rebaseBeforePR(worktreePath, issueNumber, packageManager, verbose) {
-    if (verbose) {
-        console.log(chalk.gray(`    🔄 Rebasing #${issueNumber} onto origin/main before PR...`));
-    }
-    // Fetch latest main to ensure we're rebasing onto fresh state
-    const fetchResult = spawnSync("git", ["-C", worktreePath, "fetch", "origin", "main"], {
-        stdio: "pipe",
-    });
-    if (fetchResult.status !== 0) {
-        const error = fetchResult.stderr.toString();
-        console.log(chalk.yellow(`    ⚠️  Could not fetch origin/main: ${error.trim()}`));
-        // Continue anyway - might work with local state
-    }
-    // Perform the rebase
-    const rebaseResult = spawnSync("git", ["-C", worktreePath, "rebase", "origin/main"], { stdio: "pipe" });
-    if (rebaseResult.status !== 0) {
-        const rebaseError = rebaseResult.stderr.toString();
-        // Check if it's a conflict
-        if (rebaseError.includes("CONFLICT") ||
-            rebaseError.includes("could not apply")) {
-            console.log(chalk.yellow(`    ⚠️  Rebase conflict detected. Aborting rebase and keeping original branch state.`));
-            console.log(chalk.yellow(`    ℹ️  PR will be created without rebase. Manual rebase may be required before merge.`));
-            // Abort the rebase to restore branch state
-            spawnSync("git", ["-C", worktreePath, "rebase", "--abort"], {
-                stdio: "pipe",
-            });
-            return {
-                performed: true,
-                success: false,
-                reinstalled: false,
-                error: "Rebase conflict - manual resolution required",
-            };
-        }
-        else {
-            console.log(chalk.yellow(`    ⚠️  Rebase failed: ${rebaseError.trim()}`));
-            console.log(chalk.yellow(`    ℹ️  Continuing with branch in its original state.`));
-            return {
-                performed: true,
-                success: false,
-                reinstalled: false,
-                error: rebaseError.trim(),
-            };
-        }
-    }
-    console.log(chalk.green(`    ✅ Branch rebased onto origin/main`));
-    // Check if lockfile changed and reinstall if needed
-    const reinstalled = reinstallIfLockfileChanged(worktreePath, packageManager, verbose);
-    return {
-        performed: true,
-        success: true,
-        reinstalled,
-    };
-}
-/**
- * Push branch and create a PR after successful QA.
- *
- * Handles both fresh PR creation and detection of existing PRs.
- * Failures are warnings — they don't fail the run.
- *
- * @param worktreePath Path to the worktree
- * @param issueNumber Issue number
- * @param issueTitle Issue title (for PR title)
- * @param branch Branch name
- * @param verbose Whether to show verbose output
- * @returns PRCreationResult with PR info or error
- * @internal Exported for testing
- */
-export function createPR(worktreePath, issueNumber, issueTitle, branch, verbose, labels) {
-    // Step 1: Check for existing PR on this branch
-    const existingPR = spawnSync("gh", ["pr", "view", branch, "--json", "number,url"], { stdio: "pipe", cwd: worktreePath, timeout: 15000 });
-    if (existingPR.status === 0 && existingPR.stdout) {
-        try {
-            const prInfo = JSON.parse(existingPR.stdout.toString());
-            if (prInfo.number && prInfo.url) {
-                if (verbose) {
-                    console.log(chalk.gray(`    ℹ️  PR #${prInfo.number} already exists for branch ${branch}`));
-                }
-                return {
-                    attempted: true,
-                    success: true,
-                    prNumber: prInfo.number,
-                    prUrl: prInfo.url,
-                };
-            }
-        }
-        catch {
-            // JSON parse failed — no existing PR, continue to create
-        }
-    }
-    // Step 2: Push branch to remote
-    if (verbose) {
-        console.log(chalk.gray(`    🚀 Pushing branch ${branch} to origin...`));
-    }
-    const pushResult = spawnSync("git", ["-C", worktreePath, "push", "-u", "origin", branch], { stdio: "pipe", timeout: 60000 });
-    if (pushResult.status !== 0) {
-        const pushError = pushResult.stderr?.toString().trim() ?? "Unknown error";
-        console.log(chalk.yellow(`    ⚠️  git push failed: ${pushError}`));
-        return {
-            attempted: true,
-            success: false,
-            error: `git push failed: ${pushError}`,
-        };
-    }
-    // Step 3: Create PR
-    if (verbose) {
-        console.log(chalk.gray(`    📝 Creating PR for #${issueNumber}...`));
-    }
-    const isBug = labels?.some((l) => /^bug/i.test(l));
-    const prefix = isBug ? "fix" : "feat";
-    const prTitle = `${prefix}(#${issueNumber}): ${issueTitle}`;
-    const prBody = [
-        `## Summary`,
-        ``,
-        `Automated PR for issue #${issueNumber}.`,
-        ``,
-        `Fixes #${issueNumber}`,
-        ``,
-        `---`,
-        `🤖 Generated by \`sequant run\``,
-    ].join("\n");
-    const prResult = spawnSync("gh", ["pr", "create", "--title", prTitle, "--body", prBody, "--head", branch], { stdio: "pipe", cwd: worktreePath, timeout: 30000 });
-    if (prResult.status !== 0) {
-        const prError = prResult.stderr?.toString().trim() ?? "Unknown error";
-        // Check if PR already exists (race condition or push-before-PR scenarios)
-        if (prError.includes("already exists")) {
-            const retryView = spawnSync("gh", ["pr", "view", branch, "--json", "number,url"], { stdio: "pipe", cwd: worktreePath, timeout: 15000 });
-            if (retryView.status === 0 && retryView.stdout) {
-                try {
-                    const prInfo = JSON.parse(retryView.stdout.toString());
-                    return {
-                        attempted: true,
-                        success: true,
-                        prNumber: prInfo.number,
-                        prUrl: prInfo.url,
-                    };
-                }
-                catch {
-                    // Fall through to error
-                }
-            }
-        }
-        console.log(chalk.yellow(`    ⚠️  PR creation failed: ${prError}`));
-        return {
-            attempted: true,
-            success: false,
-            error: `gh pr create failed: ${prError}`,
-        };
-    }
-    // Step 4: Extract PR URL from output and get PR details
-    const prOutput = prResult.stdout?.toString().trim() ?? "";
-    const prUrlMatch = prOutput.match(/https:\/\/github\.com\/[^\s]+\/pull\/(\d+)/);
-    if (prUrlMatch) {
-        const prNumber = parseInt(prUrlMatch[1], 10);
-        const prUrl = prUrlMatch[0];
-        console.log(chalk.green(`    ✅ PR #${prNumber} created: ${prUrl}`));
-        return {
-            attempted: true,
-            success: true,
-            prNumber,
-            prUrl,
-        };
-    }
-    // Fallback: try gh pr view to get details
-    const viewResult = spawnSync("gh", ["pr", "view", branch, "--json", "number,url"], { stdio: "pipe", cwd: worktreePath, timeout: 15000 });
-    if (viewResult.status === 0 && viewResult.stdout) {
-        try {
-            const prInfo = JSON.parse(viewResult.stdout.toString());
-            console.log(chalk.green(`    ✅ PR #${prInfo.number} created: ${prInfo.url}`));
-            return {
-                attempted: true,
-                success: true,
-                prNumber: prInfo.number,
-                prUrl: prInfo.url,
-            };
-        }
-        catch {
-            // Fall through
-        }
-    }
-    // PR was created but we couldn't parse the URL
-    console.log(chalk.yellow(`    ⚠️  PR created but could not extract URL from output: ${prOutput}`));
-    return {
-        attempted: true,
-        success: true,
-        error: "PR created but URL extraction failed",
-    };
-}
-/**
- * Natural language prompts for each phase
- * These prompts will invoke the corresponding skills via natural language
- */
-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.",
-    qa: "Review the implementation for GitHub issue #{issue} against acceptance criteria. Run the /qa {issue} workflow.",
-    loop: "Parse test/QA findings for GitHub issue #{issue} and iterate until quality gates pass. Run the /loop {issue} workflow.",
-};
-/**
- * UI-related labels that trigger automatic test phase
- */
-const UI_LABELS = ["ui", "frontend", "admin", "web", "browser"];
-/**
- * Bug-related labels that skip spec phase
- */
-const BUG_LABELS = ["bug", "fix", "hotfix", "patch"];
-/**
- * Documentation labels that skip spec phase
- */
-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)
- */
-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)));
-    // Check for docs labels → exec → qa (skip spec)
-    const isDocs = lowerLabels.some((label) => DOCS_LABELS.some((docsLabel) => label.includes(docsLabel)));
-    // Check for UI labels → add test phase
-    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) {
-        // Simple workflow: exec → qa
-        phases = ["exec", "qa"];
-    }
-    else if (isUI) {
-        // UI workflow: spec → exec → test → qa
-        phases = ["spec", "exec", "test", "qa"];
-    }
-    else {
-        // 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 };
-}
-/**
- * Parse recommended workflow from /spec output
- *
- * Looks for:
- * ## Recommended Workflow
- * **Phases:** exec → qa
- * **Quality Loop:** enabled|disabled
- */
-export function parseRecommendedWorkflow(output) {
-    // Find the Recommended Workflow section
-    const workflowMatch = output.match(/## Recommended Workflow[\s\S]*?\*\*Phases:\*\*\s*([^\n]+)/i);
-    if (!workflowMatch) {
-        return null;
-    }
-    // Parse phases from "exec → qa" or "spec → exec → test → qa" format
-    const phasesStr = workflowMatch[1].trim();
-    const phaseNames = phasesStr
-        .split(/\s*→\s*|\s*->\s*|\s*,\s*/)
-        .map((p) => p.trim().toLowerCase())
-        .filter((p) => p.length > 0);
-    // Validate and convert to Phase type
-    const validPhases = [];
-    for (const name of phaseNames) {
-        if ([
-            "spec",
-            "security-review",
-            "testgen",
-            "exec",
-            "test",
-            "qa",
-            "loop",
-        ].includes(name)) {
-            validPhases.push(name);
-        }
-    }
-    if (validPhases.length === 0) {
-        return null;
-    }
-    // Parse quality loop setting
-    const qualityLoopMatch = output.match(/\*\*Quality Loop:\*\*\s*(enabled|disabled|true|false|yes|no)/i);
-    const qualityLoop = qualityLoopMatch
-        ? ["enabled", "true", "yes"].includes(qualityLoopMatch[1].toLowerCase())
-        : false;
-    return { phases: validPhases, qualityLoop };
-}
-/**
- * Format duration in human-readable format
- */
-function formatDuration(seconds) {
-    if (seconds < 60) {
-        return `${seconds.toFixed(1)}s`;
-    }
-    const mins = Math.floor(seconds / 60);
-    const secs = seconds % 60;
-    return `${mins}m ${secs.toFixed(0)}s`;
-}
-/**
- * Get the prompt for a phase with the issue number substituted
- */
-function getPhasePrompt(phase, issueNumber) {
-    return PHASE_PROMPTS[phase].replace(/\{issue\}/g, String(issueNumber));
-}
-/**
- * Phases that require worktree isolation (exec, test, qa)
- * Spec runs in main repo since it's planning-only
- */
-const ISOLATED_PHASES = ["exec", "test", "qa"];
-/**
- * Execute a single phase for an issue using Claude Agent SDK
- */
-async function executePhase(issueNumber, phase, config, sessionId, worktreePath, shutdownManager, spinner) {
-    const startTime = Date.now();
-    if (config.dryRun) {
-        // Dry run - just simulate
-        if (config.verbose) {
-            console.log(chalk.gray(`    Would execute: /${phase} ${issueNumber}`));
-        }
-        return {
-            phase,
-            success: true,
-            durationSeconds: 0,
-        };
-    }
-    const prompt = getPhasePrompt(phase, issueNumber);
-    if (config.verbose) {
-        console.log(chalk.gray(`    Prompt: ${prompt}`));
-        if (worktreePath && ISOLATED_PHASES.includes(phase)) {
-            console.log(chalk.gray(`    Worktree: ${worktreePath}`));
-        }
-    }
-    // Determine working directory and environment
-    const shouldUseWorktree = worktreePath && ISOLATED_PHASES.includes(phase);
-    const cwd = shouldUseWorktree ? worktreePath : process.cwd();
-    // Track stderr for error diagnostics (declared outside try for catch access)
-    let capturedStderr = "";
-    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;
-        let capturedOutput = "";
-        // Build environment with worktree isolation variables
-        const env = {
-            ...process.env,
-            CLAUDE_HOOKS_SMART_TESTS: config.noSmartTests ? "false" : "true",
-        };
-        // Set worktree isolation environment variables
-        if (shouldUseWorktree) {
-            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;
-        // Get MCP servers config if enabled
-        // Reads from Claude Desktop config and passes to SDK for headless MCP support
-        const mcpServers = config.mcp ? getMcpServersConfig() : undefined;
-        // Track whether we're actively streaming verbose output
-        // Pausing spinner once per streaming session prevents truncation from rapid pause/resume cycles
-        // (Issue #283: ora's stop() clears the current line, which can truncate output when
-        // pause/resume is called for every chunk in rapid succession)
-        let verboseStreamingActive = false;
-        const queryInstance = query({
-            prompt,
-            options: {
-                abortController,
-                cwd,
-                // Load project settings including skills
-                settingSources: ["project"],
-                // Use Claude Code's system prompt and tools
-                systemPrompt: { type: "preset", preset: "claude_code" },
-                tools: { type: "preset", preset: "claude_code" },
-                // Bypass permissions for headless execution
-                permissionMode: "bypassPermissions",
-                allowDangerouslySkipPermissions: true,
-                // Resume from previous session if provided (but not when switching directories)
-                ...(canResume ? { resume: sessionId } : {}),
-                // Configure smart tests and worktree isolation via environment
-                env,
-                // Pass MCP servers for headless mode (AC-2)
-                ...(mcpServers ? { mcpServers } : {}),
-                // Capture stderr for debugging (helps diagnose early exit failures)
-                stderr: (data) => {
-                    capturedStderr += data;
-                    // Write stderr in verbose mode
-                    if (config.verbose) {
-                        // Pause spinner once to avoid truncation (Issue #283)
-                        if (!verboseStreamingActive) {
-                            spinner?.pause();
-                            verboseStreamingActive = true;
-                        }
-                        process.stderr.write(chalk.red(data));
-                    }
-                },
-            },
-        });
-        // Stream and process messages
-        for await (const message of queryInstance) {
-            // Capture session ID from system init message
-            if (message.type === "system" && message.subtype === "init") {
-                resultSessionId = message.session_id;
-            }
-            // Capture output from assistant messages
-            if (message.type === "assistant") {
-                // Extract text content from the message
-                const content = message.message.content;
-                const textContent = content
-                    .filter((c) => c.type === "text" && c.text)
-                    .map((c) => c.text)
-                    .join("");
-                if (textContent) {
-                    capturedOutput += textContent;
-                    // Show streaming output in verbose mode
-                    if (config.verbose) {
-                        // Pause spinner once at start of streaming to avoid truncation
-                        // (Issue #283: repeated pause/resume causes ora to clear lines between chunks)
-                        if (!verboseStreamingActive) {
-                            spinner?.pause();
-                            verboseStreamingActive = true;
-                        }
-                        process.stdout.write(chalk.gray(textContent));
-                    }
-                }
-            }
-            // Capture the final result
-            if (message.type === "result") {
-                resultMessage = message;
-            }
-        }
-        // Resume spinner after streaming completes (if we paused it)
-        if (verboseStreamingActive) {
-            spinner?.resume();
-            verboseStreamingActive = false;
-        }
-        clearTimeout(timeoutId);
-        // Clear abort controller from shutdown manager
-        if (shutdownManager) {
-            shutdownManager.clearAbortController();
-        }
-        const durationSeconds = (Date.now() - startTime) / 1000;
-        // Check result status
-        if (resultMessage) {
-            if (resultMessage.subtype === "success") {
-                // For QA phase, check the verdict to determine actual success
-                // SDK "success" just means the query completed - we need to parse the verdict
-                if (phase === "qa" && capturedOutput) {
-                    const verdict = parseQaVerdict(capturedOutput);
-                    // Only READY_FOR_MERGE and NEEDS_VERIFICATION are considered passing
-                    // NEEDS_VERIFICATION is external verification, not a code quality issue
-                    if (verdict &&
-                        verdict !== "READY_FOR_MERGE" &&
-                        verdict !== "NEEDS_VERIFICATION") {
-                        return {
-                            phase,
-                            success: false,
-                            durationSeconds,
-                            error: `QA verdict: ${verdict}`,
-                            sessionId: resultSessionId,
-                            output: capturedOutput,
-                            verdict, // Include parsed verdict
-                        };
-                    }
-                    // Pass case - include verdict for logging
-                    return {
-                        phase,
-                        success: true,
-                        durationSeconds,
-                        sessionId: resultSessionId,
-                        output: capturedOutput,
-                        verdict: verdict ?? undefined, // Include if found
-                    };
-                }
-                return {
-                    phase,
-                    success: true,
-                    durationSeconds,
-                    sessionId: resultSessionId,
-                    output: capturedOutput,
-                };
-            }
-            else {
-                // Handle error subtypes
-                const errorSubtype = resultMessage.subtype;
-                if (errorSubtype === "error_max_turns") {
-                    lastError = "Max turns reached";
-                }
-                else if (errorSubtype === "error_during_execution") {
-                    lastError =
-                        resultMessage.errors?.join(", ") || "Error during execution";
-                }
-                else if (errorSubtype === "error_max_budget_usd") {
-                    lastError = "Budget limit exceeded";
-                }
-                else {
-                    lastError = `Error: ${errorSubtype}`;
-                }
-                return {
-                    phase,
-                    success: false,
-                    durationSeconds,
-                    error: lastError,
-                    sessionId: resultSessionId,
-                };
-            }
-        }
-        // No result message received
-        return {
-            phase,
-            success: false,
-            durationSeconds: (Date.now() - startTime) / 1000,
-            error: "No result received from Claude",
-            sessionId: resultSessionId,
-        };
-    }
-    catch (err) {
-        const durationSeconds = (Date.now() - startTime) / 1000;
-        const error = err instanceof Error ? err.message : String(err);
-        // Check if it was an abort (timeout)
-        if (error.includes("abort") || error.includes("AbortError")) {
-            return {
-                phase,
-                success: false,
-                durationSeconds,
-                error: `Timeout after ${config.phaseTimeout}s`,
-            };
-        }
-        // Include stderr in error message if available (helps diagnose early exit failures)
-        const stderrSuffix = capturedStderr
-            ? `\nStderr: ${capturedStderr.slice(0, 500)}`
-            : "";
-        return {
-            phase,
-            success: false,
-            durationSeconds,
-            error: error + stderrSuffix,
-        };
-    }
-}
-/**
- * Cold-start retry threshold in seconds.
- * Failures under this duration are likely Claude Code subprocess initialization
- * issues rather than genuine phase failures (based on empirical data: cold-start
- * failures consistently complete in 15-39s vs 150-310s for real work).
- */
-const COLD_START_THRESHOLD_SECONDS = 60;
-const COLD_START_MAX_RETRIES = 2;
-/**
- * Execute a phase with automatic retry for cold-start failures and MCP fallback.
- *
- * Retry strategy:
- * 1. If phase fails within COLD_START_THRESHOLD_SECONDS, retry up to COLD_START_MAX_RETRIES times
- * 2. If still failing and MCP is enabled, retry once with MCP disabled (npx-based MCP servers
- *    can fail on first run due to cold-cache issues)
- *
- * The MCP fallback is safe because MCP servers are optional enhancements, not required
- * for core functionality.
- */
-/**
- * @internal Exported for testing only
- */
-export async function executePhaseWithRetry(issueNumber, phase, config, sessionId, worktreePath, shutdownManager, spinner, 
-/** @internal Injected for testing — defaults to module-level executePhase */
-executePhaseFn = executePhase) {
-    // Skip retry logic if explicitly disabled
-    if (config.retry === false) {
-        return executePhaseFn(issueNumber, phase, config, sessionId, worktreePath, shutdownManager, spinner);
-    }
-    let lastResult;
-    // Phase 1: Cold-start retry attempts (with MCP enabled if configured)
-    for (let attempt = 0; attempt <= COLD_START_MAX_RETRIES; attempt++) {
-        lastResult = await executePhaseFn(issueNumber, phase, config, sessionId, worktreePath, shutdownManager, spinner);
-        const duration = lastResult.durationSeconds ?? 0;
-        // Success or genuine failure (took long enough to be real work)
-        if (lastResult.success || duration >= COLD_START_THRESHOLD_SECONDS) {
-            return lastResult;
-        }
-        // Cold-start failure detected — retry
-        if (attempt < COLD_START_MAX_RETRIES) {
-            if (config.verbose) {
-                console.log(chalk.yellow(`\n    ⟳ Cold-start failure detected (${duration.toFixed(1)}s), retrying... (attempt ${attempt + 2}/${COLD_START_MAX_RETRIES + 1})`));
-            }
-        }
-    }
-    // Capture the original error for better diagnostics
-    const originalError = lastResult.error;
-    // Phase 2: MCP fallback - if MCP is enabled and we're still failing, try without MCP
-    // This handles npx-based MCP servers that fail on first run due to cold-cache issues
-    if (config.mcp && !lastResult.success) {
-        console.log(chalk.yellow(`\n    ⚠️ Phase failed with MCP enabled, retrying without MCP...`));
-        // Create config copy with MCP disabled
-        const configWithoutMcp = {
-            ...config,
-            mcp: false,
-        };
-        const retryResult = await executePhaseFn(issueNumber, phase, configWithoutMcp, sessionId, worktreePath, shutdownManager, spinner);
-        if (retryResult.success) {
-            console.log(chalk.green(`    ✓ Phase succeeded without MCP (MCP cold-start issue detected)`));
-            return retryResult;
-        }
-        // Both attempts failed - return original error for better diagnostics
-        return {
-            ...lastResult,
-            error: originalError,
-        };
-    }
-    return lastResult;
-}
-/**
- * Fetch issue info from GitHub
- */
-async function getIssueInfo(issueNumber) {
-    try {
-        const result = spawnSync("gh", ["issue", "view", String(issueNumber), "--json", "title,labels"], { stdio: "pipe" });
-        if (result.status === 0) {
-            const data = JSON.parse(result.stdout.toString());
-            return {
-                title: data.title || `Issue #${issueNumber}`,
-                labels: Array.isArray(data.labels)
-                    ? data.labels.map((l) => l.name)
-                    : [],
-            };
-        }
-    }
-    catch {
-        // Ignore errors, use defaults
-    }
-    return { title: `Issue #${issueNumber}`, labels: [] };
-}
-/**
- * Parse dependencies from issue body and labels
- * Returns array of issue numbers this issue depends on
- */
-function parseDependencies(issueNumber) {
-    try {
-        const result = spawnSync("gh", ["issue", "view", String(issueNumber), "--json", "body,labels"], { stdio: "pipe" });
-        if (result.status !== 0)
-            return [];
-        const data = JSON.parse(result.stdout.toString());
-        const dependencies = [];
-        // Parse from body: "Depends on: #123" or "**Depends on**: #123"
-        if (data.body) {
-            const bodyMatch = data.body.match(/\*?\*?depends\s+on\*?\*?:?\s*#?(\d+)/gi);
-            if (bodyMatch) {
-                for (const match of bodyMatch) {
-                    const numMatch = match.match(/(\d+)/);
-                    if (numMatch) {
-                        dependencies.push(parseInt(numMatch[1], 10));
-                    }
-                }
-            }
-        }
-        // Parse from labels: "depends-on/123" or "depends-on-123"
-        if (data.labels && Array.isArray(data.labels)) {
-            for (const label of data.labels) {
-                const labelName = label.name || label;
-                const labelMatch = labelName.match(/depends-on[-/](\d+)/i);
-                if (labelMatch) {
-                    dependencies.push(parseInt(labelMatch[1], 10));
-                }
-            }
-        }
-        return [...new Set(dependencies)]; // Remove duplicates
-    }
-    catch {
-        return [];
-    }
-}
-/**
- * Sort issues by dependencies (topological sort)
- * Issues with no dependencies come first, then issues that depend on them
- */
-function sortByDependencies(issueNumbers) {
-    // Build dependency graph
-    const dependsOn = new Map();
-    for (const issue of issueNumbers) {
-        const deps = parseDependencies(issue);
-        // Only include dependencies that are in our issue list
-        dependsOn.set(issue, deps.filter((d) => issueNumbers.includes(d)));
-    }
-    // Topological sort using Kahn's algorithm
-    const inDegree = new Map();
-    for (const issue of issueNumbers) {
-        inDegree.set(issue, 0);
-    }
-    for (const deps of dependsOn.values()) {
-        for (const dep of deps) {
-            inDegree.set(dep, (inDegree.get(dep) || 0) + 1);
-        }
-    }
-    // Note: inDegree counts how many issues depend on each issue
-    // We want to process issues that nothing depends on last
-    // So we sort by: issues nothing depends on first, then dependent issues
-    const sorted = [];
-    const queue = [];
-    // Start with issues that have no dependencies
-    for (const issue of issueNumbers) {
-        const deps = dependsOn.get(issue) || [];
-        if (deps.length === 0) {
-            queue.push(issue);
-        }
-    }
-    const visited = new Set();
-    while (queue.length > 0) {
-        const issue = queue.shift();
-        if (visited.has(issue))
-            continue;
-        visited.add(issue);
-        sorted.push(issue);
-        // Find issues that depend on this one
-        for (const [other, deps] of dependsOn.entries()) {
-            if (deps.includes(issue) && !visited.has(other)) {
-                // Check if all dependencies of 'other' are satisfied
-                const allDepsSatisfied = deps.every((d) => visited.has(d));
-                if (allDepsSatisfied) {
-                    queue.push(other);
-                }
-            }
-        }
-    }
-    // Add any remaining issues (circular dependencies or unvisited)
-    for (const issue of issueNumbers) {
-        if (!visited.has(issue)) {
-            sorted.push(issue);
-        }
-    }
-    return sorted;
-}
-/**
- * Check if an issue has UI-related labels
- */
-function hasUILabels(labels) {
-    return labels.some((label) => UI_LABELS.some((uiLabel) => label.toLowerCase().includes(uiLabel)));
-}
-/**
- * Determine phases to run based on options and issue labels
- */
-function determinePhasesForIssue(basePhases, labels, options) {
-    const phases = [...basePhases];
-    // Add testgen phase after spec if requested
-    if (options.testgen && phases.includes("spec")) {
-        const specIndex = phases.indexOf("spec");
-        if (!phases.includes("testgen")) {
-            phases.splice(specIndex + 1, 0, "testgen");
-        }
-    }
-    // Auto-detect UI issues and add test phase
-    if (hasUILabels(labels) && !phases.includes("test")) {
-        // Add test phase before qa if present, otherwise at the end
-        const qaIndex = phases.indexOf("qa");
-        if (qaIndex !== -1) {
-            phases.splice(qaIndex, 0, "test");
-        }
-        else {
-            phases.push("test");
-        }
-    }
-    return phases;
-}
-/**
- * Parse environment variables for CI configuration
- */
-function getEnvConfig() {
-    const config = {};
-    if (process.env.SEQUANT_QUALITY_LOOP === "true") {
-        config.qualityLoop = true;
-    }
-    if (process.env.SEQUANT_MAX_ITERATIONS) {
-        const maxIter = parseInt(process.env.SEQUANT_MAX_ITERATIONS, 10);
-        if (!isNaN(maxIter)) {
-            config.maxIterations = maxIter;
-        }
-    }
-    if (process.env.SEQUANT_SMART_TESTS === "false") {
-        config.noSmartTests = true;
-    }
-    if (process.env.SEQUANT_TESTGEN === "true") {
-        config.testgen = true;
-    }
-    return config;
-}
-/**
- * Parse batch arguments into groups of issues
- */
-function parseBatches(batchArgs) {
-    return batchArgs.map((batch) => batch
-        .split(/\s+/)
-        .map((n) => parseInt(n, 10))
-        .filter((n) => !isNaN(n)));
-}
+// Extracted modules
+import { detectDefaultBranch, ensureWorktrees, ensureWorktreesChain, getWorktreeDiffStats, } from "../lib/workflow/worktree-manager.js";
+import { formatDuration } from "../lib/workflow/phase-executor.js";
+import { getIssueInfo, sortByDependencies, parseBatches, getEnvConfig, executeBatch, runIssueWithLogging, } from "../lib/workflow/batch-executor.js";
+// Re-export public API for backwards compatibility
+export { parseQaVerdict, formatDuration, executePhaseWithRetry, } from "../lib/workflow/phase-executor.js";
+export { detectDefaultBranch, checkWorktreeFreshness, removeStaleWorktree, listWorktrees, getWorktreeChangedFiles, getWorktreeDiffStats, readCacheMetrics, filterResumedPhases, ensureWorktree, createCheckpointCommit, reinstallIfLockfileChanged, rebaseBeforePR, createPR, } from "../lib/workflow/worktree-manager.js";
+export { detectPhasesFromLabels, parseRecommendedWorkflow, determinePhasesForIssue, } from "../lib/workflow/phase-mapper.js";
+export { getIssueInfo, sortByDependencies, parseBatches, getEnvConfig, executeBatch, runIssueWithLogging, } from "../lib/workflow/batch-executor.js";
 /**
  * Main run command
  */
@@ -1610,8 +90,10 @@ export async function runCommand(issues, options) {
     // Determine if we should auto-detect phases from labels
     const autoDetectPhases = !options.phases && settings.run.autoDetectPhases;
     mergedOptions.autoDetectPhases = autoDetectPhases;
-    // Resolve base branch: CLI flag → settings.run.defaultBase → 'main'
-    const resolvedBaseBranch = options.base ?? settings.run.defaultBase ?? undefined;
+    // Resolve base branch: CLI flag → settings.run.defaultBase → auto-detect → 'main'
+    const resolvedBaseBranch = options.base ??
+        settings.run.defaultBase ??
+        detectDefaultBranch(mergedOptions.verbose ?? false);
     // Parse issue numbers (or use batch mode)
     let issueNumbers;
     let batches = null;
@@ -1886,7 +368,7 @@ export async function runCommand(issues, options) {
             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, stateManager, mergedOptions, issueInfoMap, worktreeMap, shutdown, manifest.packageManager);
+                const batchResults = await executeBatch(batch, config, logWriter, stateManager, mergedOptions, issueInfoMap, worktreeMap, shutdown, manifest.packageManager, resolvedBaseBranch);
                 results.push(...batchResults);
                 // Check if batch failed and we should stop
                 const batchFailed = batchResults.some((r) => !r.success);
@@ -1912,7 +394,7 @@ export async function runCommand(issues, options) {
                 const result = await runIssueWithLogging(issueNumber, config, logWriter, stateManager, issueInfo.title, issueInfo.labels, mergedOptions, worktreeInfo?.path, worktreeInfo?.branch, shutdown, mergedOptions.chain, // Enable checkpoint commits in chain mode
                 manifest.packageManager, 
                 // In chain mode, only the last issue should trigger pre-PR rebase
-                mergedOptions.chain ? i === issueNumbers.length - 1 : undefined);
+                mergedOptions.chain ? i === issueNumbers.length - 1 : undefined, resolvedBaseBranch);
                 results.push(result);
                 // Record PR info in log before completing issue
                 if (logWriter && result.prNumber && result.prUrl) {
@@ -1972,7 +454,7 @@ export async function runCommand(issues, options) {
                     logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
                 }
                 const result = await runIssueWithLogging(issueNumber, config, logWriter, stateManager, issueInfo.title, issueInfo.labels, mergedOptions, worktreeInfo?.path, worktreeInfo?.branch, shutdown, false, // Parallel mode doesn't support chain
-                manifest.packageManager);
+                manifest.packageManager, undefined, resolvedBaseBranch);
                 results.push(result);
                 // Record PR info in log before completing issue
                 if (logWriter && result.prNumber && result.prUrl) {
@@ -2147,418 +629,3 @@ export async function runCommand(issues, options) {
         process.exit(exitCode);
     }
 }
-/**
- * Execute a batch of issues
- */
-async function executeBatch(issueNumbers, config, logWriter, stateManager, options, issueInfoMap, worktreeMap, shutdownManager, packageManager) {
-    const results = [];
-    for (const issueNumber of issueNumbers) {
-        // Check if shutdown was triggered
-        if (shutdownManager?.shuttingDown) {
-            break;
-        }
-        const issueInfo = issueInfoMap.get(issueNumber) ?? {
-            title: `Issue #${issueNumber}`,
-            labels: [],
-        };
-        const worktreeInfo = worktreeMap.get(issueNumber);
-        // Start issue logging
-        if (logWriter) {
-            logWriter.startIssue(issueNumber, issueInfo.title, issueInfo.labels);
-        }
-        const result = await runIssueWithLogging(issueNumber, config, logWriter, stateManager, issueInfo.title, issueInfo.labels, options, worktreeInfo?.path, worktreeInfo?.branch, shutdownManager, false, // Batch mode doesn't support chain
-        packageManager);
-        results.push(result);
-        // Record PR info in log before completing issue
-        if (logWriter && result.prNumber && result.prUrl) {
-            logWriter.setPRInfo(result.prNumber, result.prUrl);
-        }
-        // Complete issue logging
-        if (logWriter) {
-            logWriter.completeIssue();
-        }
-    }
-    return results;
-}
-/**
- * Execute all phases for a single issue with logging and quality loop
- */
-async function runIssueWithLogging(issueNumber, config, logWriter, stateManager, issueTitle, labels, options, worktreePath, branch, shutdownManager, chainMode, packageManager, isLastInChain) {
-    const startTime = Date.now();
-    const phaseResults = [];
-    let loopTriggered = false;
-    let sessionId;
-    console.log(chalk.blue(`\n  Issue #${issueNumber}`));
-    if (worktreePath) {
-        console.log(chalk.gray(`    Worktree: ${worktreePath}`));
-    }
-    // Initialize state tracking for this issue
-    if (stateManager) {
-        try {
-            const existingState = await stateManager.getIssueState(issueNumber);
-            if (!existingState) {
-                await stateManager.initializeIssue(issueNumber, issueTitle, {
-                    worktree: worktreePath,
-                    branch,
-                    qualityLoop: config.qualityLoop,
-                    maxIterations: config.maxIterations,
-                });
-            }
-            else {
-                // Update worktree info if it changed
-                if (worktreePath && branch) {
-                    await stateManager.updateWorktreeInfo(issueNumber, worktreePath, branch);
-                }
-            }
-        }
-        catch (error) {
-            // State tracking errors shouldn't stop execution
-            if (config.verbose) {
-                console.log(chalk.yellow(`    ⚠️  State tracking error: ${error}`));
-            }
-        }
-    }
-    // Determine phases for this specific issue
-    let phases;
-    let detectedQualityLoop = false;
-    let specAlreadyRan = false;
-    if (options.autoDetectPhases) {
-        // Check if labels indicate a simple bug/fix (skip spec entirely)
-        const lowerLabels = labels.map((l) => l.toLowerCase());
-        const isSimpleBugFix = lowerLabels.some((label) => BUG_LABELS.some((bugLabel) => label.includes(bugLabel)));
-        if (isSimpleBugFix) {
-            // Simple bug fix: skip spec, go straight to exec → qa
-            phases = ["exec", "qa"];
-            console.log(chalk.gray(`    Bug fix detected: ${phases.join(" → ")}`));
-        }
-        else {
-            // Run spec first to get recommended workflow
-            console.log(chalk.gray(`    Running spec to determine workflow...`));
-            // Create spinner for spec phase (1 of estimated 3: spec, exec, qa)
-            const specSpinner = new PhaseSpinner({
-                phase: "spec",
-                phaseIndex: 1,
-                totalPhases: 3, // Estimate; will be refined after spec
-                shutdownManager,
-            });
-            specSpinner.start();
-            // Track spec phase start in state
-            if (stateManager) {
-                try {
-                    await stateManager.updatePhaseStatus(issueNumber, "spec", "in_progress");
-                }
-                catch {
-                    // State tracking errors shouldn't stop execution
-                }
-            }
-            const specStartTime = new Date();
-            // Note: spec runs in main repo (not worktree) for planning
-            const specResult = await executePhaseWithRetry(issueNumber, "spec", config, sessionId, worktreePath, // Will be ignored for spec (non-isolated phase)
-            shutdownManager, specSpinner);
-            const specEndTime = new Date();
-            if (specResult.sessionId) {
-                sessionId = specResult.sessionId;
-                // Update session ID in state for resume capability
-                if (stateManager) {
-                    try {
-                        await stateManager.updateSessionId(issueNumber, specResult.sessionId);
-                    }
-                    catch {
-                        // State tracking errors shouldn't stop execution
-                    }
-                }
-            }
-            phaseResults.push(specResult);
-            specAlreadyRan = true;
-            // Log spec phase result
-            // Note: Spec runs in main repo, not worktree, so no git diff stats
-            if (logWriter) {
-                const phaseLog = createPhaseLogFromTiming("spec", issueNumber, specStartTime, specEndTime, specResult.success
-                    ? "success"
-                    : specResult.error?.includes("Timeout")
-                        ? "timeout"
-                        : "failure", { error: specResult.error });
-                logWriter.logPhase(phaseLog);
-            }
-            // Track spec phase completion in state
-            if (stateManager) {
-                try {
-                    const phaseStatus = specResult.success ? "completed" : "failed";
-                    await stateManager.updatePhaseStatus(issueNumber, "spec", phaseStatus, {
-                        error: specResult.error,
-                    });
-                }
-                catch {
-                    // State tracking errors shouldn't stop execution
-                }
-            }
-            if (!specResult.success) {
-                specSpinner.fail(specResult.error);
-                const durationSeconds = (Date.now() - startTime) / 1000;
-                return {
-                    issueNumber,
-                    success: false,
-                    phaseResults,
-                    durationSeconds,
-                    loopTriggered: false,
-                };
-            }
-            specSpinner.succeed();
-            // Parse recommended workflow from spec output
-            const parsedWorkflow = specResult.output
-                ? parseRecommendedWorkflow(specResult.output)
-                : null;
-            if (parsedWorkflow) {
-                // Remove spec from phases since we already ran it
-                phases = parsedWorkflow.phases.filter((p) => p !== "spec");
-                detectedQualityLoop = parsedWorkflow.qualityLoop;
-                console.log(chalk.gray(`    Spec recommends: ${phases.join(" → ")}${detectedQualityLoop ? " (quality loop)" : ""}`));
-            }
-            else {
-                // Fall back to label-based detection
-                console.log(chalk.yellow(`    Could not parse spec recommendation, using label-based detection`));
-                const detected = detectPhasesFromLabels(labels);
-                phases = detected.phases.filter((p) => p !== "spec");
-                detectedQualityLoop = detected.qualityLoop;
-                console.log(chalk.gray(`    Fallback: ${phases.join(" → ")}`));
-            }
-        }
-    }
-    else {
-        // Use explicit phases with adjustments
-        phases = determinePhasesForIssue(config.phases, labels, options);
-        if (phases.length !== config.phases.length) {
-            console.log(chalk.gray(`    Phases adjusted: ${phases.join(" → ")}`));
-        }
-    }
-    // Resume: filter out completed phases if --resume flag is set
-    if (options.resume) {
-        const resumeResult = filterResumedPhases(issueNumber, phases, true);
-        if (resumeResult.skipped.length > 0) {
-            console.log(chalk.gray(`    Resume: skipping completed phases: ${resumeResult.skipped.join(", ")}`));
-            phases = resumeResult.phases;
-        }
-        // Also skip spec if it was auto-detected as completed
-        if (specAlreadyRan &&
-            resumeResult.skipped.length === 0 &&
-            resumeResult.phases.length === 0) {
-            console.log(chalk.gray(`    Resume: all phases already completed`));
-        }
-    }
-    // Add testgen phase if requested (and spec was in the phases)
-    if (options.testgen &&
-        (phases.includes("spec") || specAlreadyRan) &&
-        !phases.includes("testgen")) {
-        // Insert testgen at the beginning if spec already ran, otherwise after spec
-        if (specAlreadyRan) {
-            phases.unshift("testgen");
-        }
-        else {
-            const specIndex = phases.indexOf("spec");
-            if (specIndex !== -1) {
-                phases.splice(specIndex + 1, 0, "testgen");
-            }
-        }
-    }
-    let iteration = 0;
-    const useQualityLoop = config.qualityLoop || detectedQualityLoop;
-    const maxIterations = useQualityLoop ? config.maxIterations : 1;
-    let completedSuccessfully = false;
-    while (iteration < maxIterations) {
-        iteration++;
-        if (useQualityLoop && iteration > 1) {
-            console.log(chalk.yellow(`    Quality loop iteration ${iteration}/${maxIterations}`));
-            loopTriggered = true;
-        }
-        let phasesFailed = false;
-        // Calculate total phases for progress indicator
-        // If spec already ran in auto-detect mode, it's counted separately
-        const totalPhases = specAlreadyRan ? phases.length + 1 : phases.length;
-        const phaseIndexOffset = specAlreadyRan ? 1 : 0;
-        for (let phaseIdx = 0; phaseIdx < phases.length; phaseIdx++) {
-            const phase = phases[phaseIdx];
-            const phaseNumber = phaseIdx + 1 + phaseIndexOffset;
-            // Create spinner for this phase
-            const phaseSpinner = new PhaseSpinner({
-                phase,
-                phaseIndex: phaseNumber,
-                totalPhases,
-                shutdownManager,
-                iteration: useQualityLoop ? iteration : undefined,
-            });
-            phaseSpinner.start();
-            // Track phase start in state
-            if (stateManager) {
-                try {
-                    await stateManager.updatePhaseStatus(issueNumber, phase, "in_progress");
-                }
-                catch {
-                    // State tracking errors shouldn't stop execution
-                }
-            }
-            const phaseStartTime = new Date();
-            const result = await executePhaseWithRetry(issueNumber, phase, config, sessionId, worktreePath, shutdownManager, phaseSpinner);
-            const phaseEndTime = new Date();
-            // Capture session ID for subsequent phases
-            if (result.sessionId) {
-                sessionId = result.sessionId;
-                // Update session ID in state for resume capability
-                if (stateManager) {
-                    try {
-                        await stateManager.updateSessionId(issueNumber, result.sessionId);
-                    }
-                    catch {
-                        // State tracking errors shouldn't stop execution
-                    }
-                }
-            }
-            phaseResults.push(result);
-            // Log phase result with observability data (AC-1, AC-2, AC-3, AC-7)
-            if (logWriter) {
-                // Capture git diff stats for worktree phases (AC-1, AC-3)
-                const diffStats = worktreePath
-                    ? getGitDiffStats(worktreePath)
-                    : undefined;
-                // Capture commit hash after phase (AC-2)
-                const commitHash = worktreePath
-                    ? getCommitHash(worktreePath)
-                    : undefined;
-                // Read cache metrics for QA phase (AC-7)
-                const cacheMetrics = phase === "qa" ? readCacheMetrics(worktreePath) : undefined;
-                const phaseLog = createPhaseLogFromTiming(phase, issueNumber, phaseStartTime, phaseEndTime, result.success
-                    ? "success"
-                    : result.error?.includes("Timeout")
-                        ? "timeout"
-                        : "failure", {
-                    error: result.error,
-                    verdict: result.verdict,
-                    // Observability fields (AC-1, AC-2, AC-3, AC-7)
-                    filesModified: diffStats?.filesModified,
-                    fileDiffStats: diffStats?.fileDiffStats,
-                    commitHash,
-                    cacheMetrics,
-                });
-                logWriter.logPhase(phaseLog);
-            }
-            // Track phase completion in state
-            if (stateManager) {
-                try {
-                    const phaseStatus = result.success
-                        ? "completed"
-                        : result.error?.includes("Timeout")
-                            ? "failed"
-                            : "failed";
-                    await stateManager.updatePhaseStatus(issueNumber, phase, phaseStatus, { error: result.error });
-                }
-                catch {
-                    // State tracking errors shouldn't stop execution
-                }
-            }
-            if (result.success) {
-                phaseSpinner.succeed();
-            }
-            else {
-                phaseSpinner.fail(result.error);
-                phasesFailed = true;
-                // If quality loop enabled, run loop phase to fix issues
-                if (useQualityLoop && iteration < maxIterations) {
-                    // Create spinner for loop phase
-                    const loopSpinner = new PhaseSpinner({
-                        phase: "loop",
-                        phaseIndex: phaseNumber,
-                        totalPhases,
-                        shutdownManager,
-                        iteration,
-                    });
-                    loopSpinner.start();
-                    const loopResult = await executePhaseWithRetry(issueNumber, "loop", config, sessionId, worktreePath, shutdownManager, loopSpinner);
-                    phaseResults.push(loopResult);
-                    if (loopResult.sessionId) {
-                        sessionId = loopResult.sessionId;
-                    }
-                    if (loopResult.success) {
-                        loopSpinner.succeed();
-                        // Continue to next iteration
-                        break;
-                    }
-                    else {
-                        loopSpinner.fail(loopResult.error);
-                    }
-                }
-                // Stop on first failure (if not in quality loop or loop failed)
-                break;
-            }
-        }
-        // If all phases passed, exit the loop
-        if (!phasesFailed) {
-            completedSuccessfully = true;
-            break;
-        }
-        // If we're not in quality loop mode, don't retry
-        if (!config.qualityLoop) {
-            break;
-        }
-    }
-    const durationSeconds = (Date.now() - startTime) / 1000;
-    // Success is determined by whether all phases completed in any iteration,
-    // not whether all accumulated phase results passed (which would fail after loop recovery)
-    const success = completedSuccessfully;
-    // Update final issue status in state
-    if (stateManager) {
-        try {
-            const finalStatus = success ? "ready_for_merge" : "in_progress";
-            await stateManager.updateIssueStatus(issueNumber, finalStatus);
-        }
-        catch {
-            // State tracking errors shouldn't stop execution
-        }
-    }
-    // Create checkpoint commit in chain mode after QA passes
-    if (success && chainMode && worktreePath) {
-        createCheckpointCommit(worktreePath, issueNumber, config.verbose);
-    }
-    // Rebase onto origin/main before PR creation (unless --no-rebase)
-    // This ensures the branch is up-to-date and prevents lockfile drift
-    // AC-1: Non-chain mode rebases onto origin/main before PR
-    // AC-2: Chain mode rebases only the final branch onto origin/main before PR
-    //        (intermediate branches must stay based on their predecessor)
-    const shouldRebase = success &&
-        worktreePath &&
-        !options.noRebase &&
-        (!chainMode || isLastInChain);
-    if (shouldRebase) {
-        rebaseBeforePR(worktreePath, issueNumber, packageManager, config.verbose);
-    }
-    // Create PR after successful QA + rebase (unless --no-pr)
-    let prNumber;
-    let prUrl;
-    const shouldCreatePR = success && worktreePath && branch && !options.noPr;
-    if (shouldCreatePR) {
-        const prResult = createPR(worktreePath, issueNumber, issueTitle, branch, config.verbose, labels);
-        if (prResult.success && prResult.prNumber && prResult.prUrl) {
-            prNumber = prResult.prNumber;
-            prUrl = prResult.prUrl;
-            // Update workflow state with PR info
-            if (stateManager) {
-                try {
-                    await stateManager.updatePRInfo(issueNumber, {
-                        number: prResult.prNumber,
-                        url: prResult.prUrl,
-                    });
-                }
-                catch {
-                    // State tracking errors shouldn't stop execution
-                }
-            }
-        }
-    }
-    return {
-        issueNumber,
-        success,
-        phaseResults,
-        durationSeconds,
-        loopTriggered,
-        prNumber,
-        prUrl,
-    };
-}