gsd-pi 2.80.0-dev.c2213c771 → 2.80.0-dev.c5c38454b

package/dist/resources/.managed-resources-content-hash

@@ -1 +1 @@
-4cdd0ed39f5663d1
+7088672cce649c64

package/dist/resources/extensions/github-sync/templates.js

@@ -8,6 +8,37 @@
  * for the `gh` CLI body parameters.
  */
 import { buildPrEvidence } from "../gsd/pr-evidence.js";
+// ─── Helpers ────────────────────────────────────────────────────────────────
+/**
+ * Wrap a string in a CommonMark inline-code span, escaping any embedded
+ * backticks by selecting a fence longer than the longest backtick run inside
+ * the input. If the input begins or ends with a backtick, pad with a single
+ * space inside the fence (CommonMark requirement).
+ *
+ * Empty input returns an empty string (no fence) — there is nothing to render
+ * as code, and emitting an empty pair of backticks would produce literal
+ * backticks in GitHub-flavored markdown.
+ */
+export function inlineCode(s) {
+    if (s.length === 0)
+        return "";
+    let longestRun = 0;
+    let currentRun = 0;
+    for (const ch of s) {
+        if (ch === "`") {
+            currentRun++;
+            if (currentRun > longestRun)
+                longestRun = currentRun;
+        }
+        else {
+            currentRun = 0;
+        }
+    }
+    const fence = "`".repeat(longestRun + 1);
+    const needsPad = s.startsWith("`") || s.endsWith("`");
+    const pad = needsPad ? " " : "";
+    return `${fence}${pad}${s}${pad}${fence}`;
+}
 export function formatMilestoneIssueBody(data) {
     const lines = [];
     lines.push(`# ${data.id}: ${data.title}`);
@@ -78,7 +109,7 @@ export function formatTaskIssueBody(data) {
     if (data.files?.length) {
         lines.push("### Files");
         for (const file of data.files) {
-            lines.push(`- \`${file}\``);
+            lines.push(`- ${inlineCode(file)}`);
         }
         lines.push("");
     }
@@ -132,15 +163,14 @@ export function formatSwarmLanePRBody(data) {
     const summaries = [
         [
             "### Swarm lane",
-            `**Lane:** \`${laneLabel}\``,
-            `**Branch:** \`${data.lane.branch}\``,
+            `**Lane:** ${inlineCode(laneLabel)}`,
+            `**Branch:** ${inlineCode(data.lane.branch)}`,
             data.lane.owner ? `**Owner:** ${data.lane.owner}` : "",
-            data.lane.latestCommit ? `**Latest commit:** \`${data.lane.latestCommit}\`` : "",
+            data.lane.latestCommit ? `**Latest commit:** ${inlineCode(data.lane.latestCommit)}` : "",
         ].filter(Boolean).join("\n"),
         `### Impact area\n${data.impactArea}`,
         `### Changed contracts\n${checkedList(data.lane.changedContracts, "No shared contracts changed").join("\n")}`,
         `### Transition risks\n${checkedList(data.transitionRisks, "No transition risks identified").join("\n")}`,
-        data.lane.blockers?.length ? `### Blockers\n${data.lane.blockers.map((blocker) => `- ${blocker}`).join("\n")}` : "",
     ].filter(Boolean);
     return buildPrEvidence({
         milestoneId: laneLabel,
@@ -150,6 +180,7 @@ export function formatSwarmLanePRBody(data) {
         changeType: "refactor",
         linkedIssue: data.linkedIssue ? `Closes #${data.linkedIssue}` : undefined,
         summaries,
+        blockers: data.lane.blockers ?? [],
         testsRun: data.lane.testEvidence,
         rollbackNotes: data.rollbackPlan,
         how: "Generated by GSD GitHub Sync swarm routines from lane evidence.",
@@ -159,7 +190,7 @@ export function formatSwarmReleaseChecklistBody(data) {
     const lines = [];
     lines.push(`# UOK Swarm Release Checklist`);
     lines.push("");
-    lines.push(`**Integration branch:** \`${data.integrationBranch}\``);
+    lines.push(`**Integration branch:** ${inlineCode(data.integrationBranch)}`);
     lines.push("");
     lines.push("## Lane summary");
     lines.push("");
@@ -167,9 +198,9 @@ export function formatSwarmReleaseChecklistBody(data) {
     lines.push("|------|--------|-------|--------|--------|");
     for (const lane of data.lanes) {
         const owner = lane.owner ?? "";
-        const commit = lane.latestCommit ? `\`${lane.latestCommit}\`` : "";
+        const commit = lane.latestCommit ? inlineCode(lane.latestCommit) : "";
         const status = lane.blockers?.length ? "blocked" : "ready";
-        lines.push(`| \`${SWARM_LANE_LABELS[lane.id]}\` | \`${lane.branch}\` | ${owner} | ${commit} | ${status} |`);
+        lines.push(`| ${inlineCode(SWARM_LANE_LABELS[lane.id])} | ${inlineCode(lane.branch)} | ${owner} | ${commit} | ${status} |`);
     }
     lines.push("");
     lines.push("## Required evidence");

package/dist/resources/extensions/gsd/auto/loop.js

@@ -268,6 +268,19 @@ export async function autoLoop(ctx, pi, s, deps, options) {
             // ── Blanket try/catch: one bad iteration must not kill the session
             const prefs = deps.loadEffectiveGSDPreferences()?.preferences;
             const uokFlags = resolveUokFlags(prefs);
+            // ── Check sidecar queue before deriveState ──
+            // NOTE: Sidecar dequeue MUST run before validateWorkflowSessionLock so a
+            // queued item is popped (and the `sidecar-dequeue` journal event emitted)
+            // even when the session lock invalidates this iteration. Inverting this
+            // order silently drops queued items on lock-loss. Refs #5308.
+            const sidecarItem = await dequeueSidecarItem({
+                queue: s.sidecarQueue,
+                executionGraphEnabled: uokFlags.executionGraph,
+                scheduleQueue: scheduleSidecarQueue,
+                warnSchedulingFailure: message => logWarning("dispatch", `sidecar queue scheduling failed: ${message}`),
+                logDequeue: payload => debugLog("autoLoop", { phase: "sidecar-dequeue", ...payload }),
+                emitDequeue: payload => journalReporter.emit("sidecar-dequeue", payload),
+            });
             const sessionLockOutcome = validateWorkflowSessionLock({
                 active: s.active,
                 iteration,
@@ -287,17 +300,9 @@ export async function autoLoop(ctx, pi, s, deps, options) {
                 },
             });
             if (sessionLockOutcome.action === "stop" && sessionLockOutcome.reason === "session-lock-lost") {
+                finishTurn("stopped", "manual-attention", sessionLockOutcome.reason);
                 break;
             }
-            // ── Check sidecar queue before deriveState ──
-            const sidecarItem = await dequeueSidecarItem({
-                queue: s.sidecarQueue,
-                executionGraphEnabled: uokFlags.executionGraph,
-                scheduleQueue: scheduleSidecarQueue,
-                warnSchedulingFailure: message => logWarning("dispatch", `sidecar queue scheduling failed: ${message}`),
-                logDequeue: payload => debugLog("autoLoop", { phase: "sidecar-dequeue", ...payload }),
-                emitDequeue: payload => journalReporter.emit("sidecar-dequeue", payload),
-            });
             const ic = { ctx, pi, s, deps, prefs, iteration, flowId, nextSeq };
             journalReporter.emit("iteration-start", { iteration });
             let iterData;
@@ -331,6 +336,7 @@ export async function autoLoop(ctx, pi, s, deps, options) {
                     isComplete: engineState.isComplete,
                 });
                 if (engineState.isComplete) {
+                    finishTurn("completed");
                     await deps.stopAuto(ctx, pi, "Workflow complete");
                     break;
                 }
@@ -734,6 +740,7 @@ export async function autoLoop(ctx, pi, s, deps, options) {
                 });
                 if (cooldownDecision.action === "stop") {
                     ctx.ui.notify(cooldownDecision.notifyMessage, "error");
+                    finishTurn("stopped", "timeout", msg);
                     await deps.stopAuto(ctx, pi, cooldownDecision.stopMessage);
                     break;
                 }

package/dist/resources/extensions/gsd/auto/run-unit.js

@@ -1,14 +1,11 @@
-/**
- * auto/run-unit.ts — Single unit execution: session create → prompt → await agent_end.
- *
- * Imports from: auto/types, auto/resolve
- */
+// GSD-2 + src/resources/extensions/gsd/auto/run-unit.ts - Runs one GSD auto-mode unit from session creation through agent completion.
 import { NEW_SESSION_TIMEOUT_MS } from "./session.js";
 import { _clearCurrentResolve, _setCurrentResolve, _setSessionSwitchInFlight } from "./resolve.js";
 import { getCurrentTurnGeneration, runWithTurnGeneration, } from "./turn-epoch.js";
 import { debugLog } from "../debug-logger.js";
 import { logWarning } from "../workflow-logger.js";
 import { resolveAutoSupervisorConfig } from "../preferences.js";
+import { formatAutoUnitWorkingMessage } from "../working-output-messages.js";
 // Tracks the latest session-switch attempt so a late timeout settlement from an
 // older runUnit() call cannot clear the guard for a newer one.
 let sessionSwitchGeneration = 0;
@@ -151,22 +148,29 @@ export async function runUnit(ctx, pi, s, unitType, unitId, prompt) {
     // ── Send the prompt ──
     debugLog("runUnit", { phase: "send-message", unitType, unitId });
     const requestDispatchedAt = Date.now();
-    pi.sendMessage({ customType: "gsd-auto", content: prompt, display: s.verbose }, { triggerTurn: true });
+    ctx.ui.setWorkingMessage?.(formatAutoUnitWorkingMessage(unitType, unitId));
     // ── Await agent_end with absolute timeout (H4 fix) ──
     // If supervision fails to resolve unitPromise within 30s, treat as cancelled.
     // Without this, a crashed agent that never emits agent_end hangs the loop (#3161).
-    debugLog("runUnit", { phase: "awaiting-agent-end", unitType, unitId });
     const supervisor = resolveAutoSupervisorConfig();
     const UNIT_HARD_TIMEOUT_MS = Math.max(30_000, ((supervisor.hard_timeout_minutes ?? 30) * 60 * 1000) + 30_000);
     let unitTimeoutHandle;
-    const timeoutResult = new Promise((resolve) => {
-        unitTimeoutHandle = setTimeout(() => {
-            resolve({ status: "cancelled", errorContext: { message: "Unit hard timeout — supervision may have failed", category: "timeout", isTransient: true } });
-        }, UNIT_HARD_TIMEOUT_MS);
-    });
-    const result = await runWithTurnGeneration(capturedTurnGen, () => Promise.race([unitPromise, timeoutResult]));
-    if (unitTimeoutHandle)
-        clearTimeout(unitTimeoutHandle);
+    let result;
+    try {
+        pi.sendMessage({ customType: "gsd-auto", content: prompt, display: s.verbose }, { triggerTurn: true });
+        debugLog("runUnit", { phase: "awaiting-agent-end", unitType, unitId });
+        const timeoutResult = new Promise((resolve) => {
+            unitTimeoutHandle = setTimeout(() => {
+                resolve({ status: "cancelled", errorContext: { message: "Unit hard timeout — supervision may have failed", category: "timeout", isTransient: true } });
+            }, UNIT_HARD_TIMEOUT_MS);
+        });
+        result = await runWithTurnGeneration(capturedTurnGen, () => Promise.race([unitPromise, timeoutResult]));
+    }
+    finally {
+        if (unitTimeoutHandle)
+            clearTimeout(unitTimeoutHandle);
+        ctx.ui.setWorkingMessage?.(undefined);
+    }
     debugLog("runUnit", {
         phase: "agent-end-received",
         unitType,

package/dist/resources/extensions/gsd/auto-dashboard.js

@@ -1,10 +1,4 @@
-/**
- * Auto-mode Dashboard — progress widget rendering, elapsed time formatting,
- * unit description helpers, and slice progress caching.
- *
- * Pure functions that accept specific parameters — no module-level globals
- * or AutoContext dependency. State accessors are passed as callbacks.
- */
+// GSD-2 + src/resources/extensions/gsd/auto-dashboard.ts - Auto-mode progress widget rendering and dashboard helpers.
 import { getCurrentBranch } from "./worktree.js";
 import { getActiveHook } from "./post-unit-hooks.js";
 import { getLedger, getProjectTotals } from "./metrics.js";
@@ -25,6 +19,7 @@ import { formatRtkSavingsLabel, getRtkSessionSavings, } from "../shared/rtk-sess
 import { logWarning } from "./workflow-logger.js";
 import { formattedShortcutPair } from "./shortcut-defs.js";
 import { homedir } from "node:os";
+import { readUnitRuntimeRecord } from "./unit-runtime.js";
 // ─── UAT Slice Extraction ─────────────────────────────────────────────────────
 /**
  * Extract the target slice ID from a run-uat unit ID (e.g. "M001/S01" → "S01").
@@ -165,6 +160,30 @@ export function formatWidgetTokens(count) {
         return `${(count / 1000000).toFixed(1)}M`;
     return `${Math.round(count / 1000000)}M`;
 }
+export function formatRuntimeHealthSignal(record, now = Date.now()) {
+    if (!record)
+        return null;
+    const idleMs = Math.max(0, now - record.lastProgressAt);
+    const idleMinutes = Math.floor(idleMs / 60_000);
+    if ((record.recoveryAttempts ?? 0) > 0 || record.phase === "recovered" || record.lastProgressKind.includes("recovery")) {
+        return {
+            level: "yellow",
+            summary: "Recovering",
+            detail: `retry ${record.recoveryAttempts ?? 1} after ${record.lastRecoveryReason ?? "idle"} stall`,
+        };
+    }
+    if (record.progressCount === 0 && idleMs >= 60_000) {
+        return {
+            level: "yellow",
+            summary: "Waiting on provider",
+            detail: `no output for ${idleMinutes}m`,
+        };
+    }
+    return null;
+}
+export function shouldRenderRoadmapProgress(progress) {
+    return !!progress && progress.total > 0;
+}
 // ─── ETA Estimation ──────────────────────────────────────────────────────────
 /**
  * Estimate remaining time based on average unit duration from the metrics ledger.
@@ -499,6 +518,7 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
         let cachedLines;
         let cachedWidth;
         let cachedRtkLabel;
+        let cachedRuntimeRecord = null;
         const refreshRtkLabel = () => {
             try {
                 const sessionId = ctx.sessionManager.getSessionId();
@@ -510,7 +530,16 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
                 cachedRtkLabel = null;
             }
         };
+        const refreshRuntimeRecord = () => {
+            try {
+                cachedRuntimeRecord = readUnitRuntimeRecord(accessors.getBasePath(), unitType, unitId);
+            }
+            catch {
+                cachedRuntimeRecord = null;
+            }
+        };
         refreshRtkLabel();
+        refreshRuntimeRecord();
         const pulseTimer = setInterval(() => {
             pulseBright = !pulseBright;
             cachedLines = undefined;
@@ -526,6 +555,7 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
                     updateSliceProgressCache(accessors.getBasePath(), mid.id, slice?.id);
                 }
                 refreshRtkLabel();
+                refreshRuntimeRecord();
                 cachedLines = undefined;
             }
             catch (err) { /* non-fatal */
@@ -555,13 +585,16 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
                 const modeTag = accessors.isStepMode() ? "NEXT" : "AUTO";
                 // Health indicator in header
                 const score = computeProgressScore();
-                const healthColor = score.level === "green" ? "success"
-                    : score.level === "yellow" ? "warning"
+                const runtimeSignal = formatRuntimeHealthSignal(cachedRuntimeRecord);
+                const healthLevel = runtimeSignal?.level ?? score.level;
+                const healthSummary = runtimeSignal?.summary ?? score.summary;
+                const healthColor = healthLevel === "green" ? "success"
+                    : healthLevel === "yellow" ? "warning"
                         : "error";
-                const healthIcon = score.level === "green" ? GLYPH.statusActive
-                    : score.level === "yellow" ? "!"
+                const healthIcon = healthLevel === "green" ? GLYPH.statusActive
+                    : healthLevel === "yellow" ? "!"
                         : "x";
-                const healthStr = `  ${theme.fg(healthColor, healthIcon)} ${theme.fg(healthColor, score.summary)}`;
+                const healthStr = `  ${theme.fg(healthColor, healthIcon)} ${theme.fg(healthColor, healthSummary)}`;
                 const headerLeft = `${pad}${dot} ${theme.fg("accent", theme.bold("GSD"))}  ${theme.fg("success", modeTag)}${healthStr}`;
                 // ETA in header right, after elapsed
                 const eta = estimateTimeRemaining();
@@ -573,7 +606,10 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
                     : "";
                 lines.push(rightAlign(headerLeft, headerRight, width));
                 // Show health signal details when degraded (yellow/red)
-                if (score.level !== "green" && score.signals.length > 0 && widgetMode !== "min") {
+                if (runtimeSignal?.detail && widgetMode !== "min") {
+                    lines.push(`${pad}  ${theme.fg("dim", runtimeSignal.detail)}`);
+                }
+                else if (score.level !== "green" && score.signals.length > 0 && widgetMode !== "min") {
                     // Show up to 3 most relevant signals in compact form
                     const topSignals = score.signals
                         .filter(s => s.kind === "negative")
@@ -645,7 +681,7 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
                     lines.push(rightAlign(actionLeft, theme.fg("dim", phaseLabel), width));
                     // Progress bar
                     const roadmapSlices = mid ? getRoadmapSlicesSync() : null;
-                    if (roadmapSlices) {
+                    if (shouldRenderRoadmapProgress(roadmapSlices)) {
                         const { done, total, activeSliceTasks } = roadmapSlices;
                         const barWidth = Math.max(6, Math.min(18, Math.floor(width * 0.25)));
                         const pct = total > 0 ? done / total : 0;
@@ -706,7 +742,7 @@ export function updateProgressWidget(ctx, unitType, unitId, state, accessors, ti
                     ? Math.floor(width * (width >= 100 ? 0.45 : 0.50))
                     : width;
                 const leftLines = [];
-                if (roadmapSlices) {
+                if (shouldRenderRoadmapProgress(roadmapSlices)) {
                     const { done, total, activeSliceTasks } = roadmapSlices;
                     const barWidth = Math.max(6, Math.min(18, Math.floor(leftColWidth * 0.4)));
                     const pct = total > 0 ? done / total : 0;

package/dist/resources/extensions/gsd/auto-dispatch.js

@@ -93,6 +93,16 @@ export function hasPendingDeepStage(prefs, basePath) {
     const gate = getDeepStageGate(prefs, basePath);
     return gate.status === "pending" || gate.status === "blocked";
 }
+export function shouldRunDeepProjectSetup(state, prefs, basePath, options = {}) {
+    if (options.hasSurvivorBranch === true)
+        return false;
+    if (state.phase !== "pre-planning" &&
+        state.phase !== "needs-discussion" &&
+        state.phase !== "planning") {
+        return false;
+    }
+    return hasPendingDeepStage(prefs, basePath);
+}
 function missingSliceStop(mid, phase) {
     return {
         action: "stop",

package/dist/resources/extensions/gsd/auto-recovery.js

@@ -12,7 +12,7 @@ import { appendEvent } from "./workflow-events.js";
 import { atomicWriteSync } from "./atomic-write.js";
 import { clearParseCache } from "./files.js";
 import { parseRoadmap as parseLegacyRoadmap, parsePlan as parseLegacyPlan } from "./parsers-legacy.js";
-import { isDbAvailable, getTask, getSlice, getSliceTasks, getPendingGates, updateTaskStatus, updateSliceStatus, insertSlice, getMilestone, refreshOpenDatabaseFromDisk } from "./gsd-db.js";
+import { isDbAvailable, getTask, getSlice, getSliceTasks, getPendingGates, updateTaskStatus, updateSliceStatus, insertSlice, getMilestone, refreshOpenDatabaseFromDisk, getCompletedMilestoneTaskFileHints, getMilestoneCommitAttributionShas, recordMilestoneCommitAttribution } from "./gsd-db.js";
 import { isValidationTerminal } from "./state.js";
 import { getErrorMessage } from "./error-utils.js";
 import { logWarning, logError } from "./workflow-logger.js";
@@ -110,17 +110,32 @@ export function hasImplementationArtifacts(basePath, milestoneId) {
         // milestone commits instead of treating the self-diff as proof of no work.
         if (changedFiles.length === 0) {
             if (milestoneId && currentBranch === integrationBranch) {
-                const tagged = getChangedFilesFromMilestoneTaggedCommits(basePath, milestoneId);
-                if (!tagged.ok)
+                const milestoneEvidence = getChangedFilesFromMilestoneEvidence(basePath, milestoneId);
+                if (!milestoneEvidence.ok)
                     return "unknown";
-                if (tagged.matched)
-                    return classifyImplementationFiles(tagged.files);
+                if (milestoneEvidence.matched)
+                    return classifyImplementationFiles(milestoneEvidence.files);
             }
             if (currentBranch && currentBranch !== "HEAD")
                 return "absent";
             return "unknown";
         }
-        return classifyImplementationFiles(changedFiles);
+        const branchClassification = classifyImplementationFiles(changedFiles);
+        if (branchClassification === "present")
+            return "present";
+        // A completing milestone branch can have a non-empty diff containing only
+        // .gsd/ closeout files after implementation commits already landed on the
+        // recorded integration branch. In that topology, the branch diff alone is
+        // insufficient; use the same milestone-tagged evidence fallback as the
+        // self-diff retry path before declaring the milestone implementation-free.
+        if (milestoneId) {
+            const milestoneEvidence = getChangedFilesFromMilestoneEvidence(basePath, milestoneId);
+            if (!milestoneEvidence.ok)
+                return "unknown";
+            if (milestoneEvidence.matched)
+                return classifyImplementationFiles(milestoneEvidence.files);
+        }
+        return "absent";
     }
     catch (e) {
         // Non-fatal — if git operations fail, return unknown so callers can decide
@@ -148,6 +163,9 @@ function classifyImplementationFiles(files) {
 function isImplementationPath(file) {
     return !file.startsWith(".gsd/") && !file.startsWith(".gsd\\");
 }
+function normalizeRepoPath(file) {
+    return file.trim().replace(/\\/g, "/").replace(/^\.\/+/, "");
+}
 /**
  * Detect the main/master branch name.
  */
@@ -217,7 +235,7 @@ function getChangedFilesFromMilestoneTaggedCommits(basePath, milestoneId) {
     ]);
     if (!scoped.ok)
         return scoped;
-    if (scoped.matched)
+    if (scoped.matched && classifyImplementationFiles(scoped.files) === "present")
         return scoped;
     // Fallback (#5033): when .gsd/ is gitignored / external / untracked, the
     // path-scoped scan matches no commits even though GSD-tagged commits
@@ -228,9 +246,137 @@ function getChangedFilesFromMilestoneTaggedCommits(basePath, milestoneId) {
     // Intentionally unbounded — symmetric with the primary scan, and avoids
     // reintroducing the rolling-depth failure class removed in #4699 where
     // milestone evidence aged out behind unrelated activity.
-    return scanGsdTaggedCommits(basePath, milestoneId, [
+    const unscoped = scanGsdTaggedCommits(basePath, milestoneId, [
         "log", "--format=%H%x1f%B%x1e", "HEAD",
     ]);
+    if (!unscoped.ok)
+        return scoped.matched ? scoped : unscoped;
+    if (!unscoped.matched)
+        return scoped;
+    return {
+        ok: true,
+        matched: true,
+        files: [...new Set([...scoped.files, ...unscoped.files])],
+    };
+}
+function getChangedFilesFromMilestoneEvidence(basePath, milestoneId) {
+    const tagged = getChangedFilesFromMilestoneTaggedCommits(basePath, milestoneId);
+    if (!tagged.ok)
+        return tagged;
+    if (tagged.matched && classifyImplementationFiles(tagged.files) === "present")
+        return tagged;
+    const attributed = getChangedFilesFromAttributedMilestoneCommits(basePath, milestoneId);
+    if (!attributed.ok)
+        return tagged.matched ? tagged : attributed;
+    if (attributed.matched && classifyImplementationFiles(attributed.files) === "present")
+        return attributed;
+    const backfilled = backfillChangedFilesFromUntaggedMilestoneCommits(basePath, milestoneId);
+    if (!backfilled.ok)
+        return tagged.matched ? tagged : attributed.matched ? attributed : backfilled;
+    if (!backfilled.matched) {
+        if (tagged.matched)
+            return tagged;
+        return attributed.matched ? attributed : backfilled;
+    }
+    return {
+        ok: true,
+        matched: true,
+        files: [...new Set([...tagged.files, ...attributed.files, ...backfilled.files])],
+    };
+}
+function getChangedFilesFromAttributedMilestoneCommits(basePath, milestoneId) {
+    try {
+        const shas = getMilestoneCommitAttributionShas(milestoneId);
+        if (shas.length === 0)
+            return { ok: true, matched: false, files: [] };
+        const files = new Set();
+        let matched = false;
+        for (const sha of shas) {
+            if (!isFullCommitSha(sha))
+                continue;
+            const commitFiles = getChangedFilesForCommit(basePath, sha);
+            if (commitFiles.length === 0)
+                continue;
+            matched = true;
+            for (const file of commitFiles)
+                files.add(file);
+        }
+        return { ok: true, matched, files: [...files] };
+    }
+    catch (e) {
+        logWarning("recovery", `milestone attribution scan failed: ${e.message}`);
+        return { ok: false, matched: false, files: [] };
+    }
+}
+function backfillChangedFilesFromUntaggedMilestoneCommits(basePath, milestoneId) {
+    try {
+        const milestone = getMilestone(milestoneId);
+        const milestoneStartedAt = milestone?.created_at ? Math.floor(Date.parse(milestone.created_at) / 1000) * 1000 : NaN;
+        if (!Number.isFinite(milestoneStartedAt))
+            return { ok: true, matched: false, files: [] };
+        const taskFileHints = getCompletedMilestoneTaskFileHints(milestoneId);
+        if (taskFileHints.length === 0)
+            return { ok: true, matched: false, files: [] };
+        const hintSet = new Set(taskFileHints.map(normalizeRepoPath).filter(Boolean));
+        if (hintSet.size === 0)
+            return { ok: true, matched: false, files: [] };
+        const records = getCommitRecords(basePath);
+        const files = new Set();
+        let matched = false;
+        for (const record of records) {
+            if (!isFullCommitSha(record.hash))
+                continue;
+            if (Date.parse(record.committedAt) < milestoneStartedAt)
+                continue;
+            if (record.parents.trim().split(/\s+/).filter(Boolean).length > 1)
+                continue;
+            if (commitMessageHasGsdTrailer(record.message))
+                continue;
+            const commitFiles = getChangedFilesForCommit(basePath, record.hash);
+            const implementationFiles = commitFiles.map(normalizeRepoPath).filter(isImplementationPath);
+            if (implementationFiles.length === 0)
+                continue;
+            if (!implementationFiles.some((file) => hintSet.has(file)))
+                continue;
+            matched = true;
+            for (const file of implementationFiles)
+                files.add(file);
+            recordMilestoneCommitAttribution({
+                commitSha: record.hash,
+                milestoneId,
+                source: "backfill",
+                confidence: 0.8,
+                files: implementationFiles,
+                createdAt: new Date().toISOString(),
+            });
+        }
+        return { ok: true, matched, files: [...files] };
+    }
+    catch (e) {
+        logWarning("recovery", `milestone attribution backfill failed: ${e.message}`);
+        return { ok: false, matched: false, files: [] };
+    }
+}
+function getCommitRecords(basePath) {
+    const logOutput = execFileSync("git", ["log", "--format=%H%x1f%P%x1f%cI%x1f%B%x1e", "HEAD"], {
+        cwd: basePath,
+        stdio: ["ignore", "pipe", "pipe"],
+        encoding: "utf-8",
+    });
+    return logOutput
+        .split("\x1e")
+        .map((record) => record.trim())
+        .filter(Boolean)
+        .flatMap((record) => {
+        const parts = record.split("\x1f");
+        if (parts.length < 4)
+            return [];
+        const [hash, parents, committedAt, ...messageParts] = parts;
+        return [{ hash: hash.trim(), parents: parents.trim(), committedAt: committedAt.trim(), message: messageParts.join("\x1f") }];
+    });
+}
+function isFullCommitSha(value) {
+    return /^[0-9a-f]{40}$/i.test(value);
 }
 function scanGsdTaggedCommits(basePath, milestoneId, gitArgs) {
     try {

package/dist/resources/extensions/gsd/auto-start.js

@@ -487,9 +487,8 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             hasSurvivorBranch = false;
         }
         const effectivePrefs = loadEffectiveGSDPreferences(base)?.preferences;
-        const deepProjectStagePending = !hasSurvivorBranch
-            ? (await import("./auto-dispatch.js")).hasPendingDeepStage(effectivePrefs, base)
-            : false;
+        const { shouldRunDeepProjectSetup } = await import("./auto-dispatch.js");
+        const deepProjectStagePending = shouldRunDeepProjectSetup(state, effectivePrefs, base, { hasSurvivorBranch });
         if (deepProjectStagePending) {
             // Deep project-level setup runs before the first milestone exists. Let
             // the auto loop dispatch workflow-preferences / project / requirements

package/dist/resources/extensions/gsd/bootstrap/agent-end-recovery.js

@@ -1,10 +1,11 @@
+// GSD-2 + src/resources/extensions/gsd/bootstrap/agent-end-recovery.ts - Handles provider and agent-end recovery for GSD auto-mode.
 import { logWarning } from "../workflow-logger.js";
 import { checkDeepProjectSetupAfterTurn, checkAutoStartAfterDiscuss, maybeHandleReadyPhraseWithoutFiles, maybeHandleEmptyIntentTurn, resetEmptyTurnCounter, } from "../guided-flow.js";
 import { clearPathCache } from "../paths.js";
 import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto, setCurrentDispatchedModelId } from "../auto.js";
 import { getNextFallbackModel, resolveModelWithFallbacksForUnit } from "../preferences.js";
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
-import { isSessionSwitchInFlight, resolveAgentEnd } from "../auto/resolve.js";
+import { isSessionSwitchInFlight, resolveAgentEnd, resolveAgentEndCancelled } from "../auto/resolve.js";
 import { resolveModelId } from "../auto-model-selection.js";
 import { resolveProjectRoot } from "../worktree.js";
 import { clearDiscussionFlowState } from "./write-gate.js";
@@ -47,6 +48,11 @@ export function _buildAbortedPauseContext(lastMsg) {
         isTransient: true,
     };
 }
+export function isUserInitiatedAbortMessage(message) {
+    if (!message)
+        return false;
+    return /\b(?:claude code process aborted by user|request aborted by user|process aborted by user)\b/i.test(message);
+}
 async function pauseTransientWithBackoff(cls, pi, ctx, errorDetail, isRateLimit) {
     retryState.consecutiveTransientCount += 1;
     const baseRetryAfterMs = "retryAfterMs" in cls ? cls.retryAfterMs : 15_000;
@@ -150,6 +156,14 @@ export async function handleAgentEnd(pi, event, ctx) {
         // is in the assistant message text content. Fall back to content when
         // errorMessage looks uninformative.
         const rawErrorMsg = ("errorMessage" in lastMsg && lastMsg.errorMessage) ? String(lastMsg.errorMessage) : "";
+        if (isUserInitiatedAbortMessage(rawErrorMsg)) {
+            resolveAgentEndCancelled({
+                message: rawErrorMsg,
+                category: "aborted",
+                isTransient: false,
+            });
+            return;
+        }
         const isUseless = !rawErrorMsg || /^(success|ok|true|error|unknown)$/i.test(rawErrorMsg.trim());
         // #3588: When errorMessage is uninformative, extract the real error from
         // the assistant message text content for display purposes only.

package/dist/resources/extensions/gsd/bootstrap/register-hooks.js

@@ -2,7 +2,7 @@ import { join } from "node:path";
 import { isToolCallEventType } from "@gsd/pi-coding-agent";
 import { updateSnapshot } from "../ecosystem/gsd-extension-api.js";
 import { buildMilestoneFileName, resolveMilestonePath, resolveSliceFile, resolveSlicePath } from "../paths.js";
-import { canonicalToolName, clearDiscussionFlowState, isDepthConfirmationAnswer, isQueuePhaseActive, markApprovalGateVerified, markDepthVerified, resetWriteGateState, shouldBlockContextWrite, shouldBlockPlanningUnit, shouldBlockQueueExecution, isGateQuestionId, setPendingGate, clearPendingGate, getPendingGate, shouldBlockPendingGate, shouldBlockPendingGateBash, extractDepthVerificationMilestoneId } from "./write-gate.js";
+import { canonicalToolName, clearDiscussionFlowState, isDepthConfirmationAnswer, isQueuePhaseActive, markApprovalGateVerified, markDepthVerified, resetWriteGateState, shouldBlockContextWrite, shouldBlockPlanningUnit, shouldBlockQueueExecution, shouldBlockWorktreeWrite, isGateQuestionId, setPendingGate, clearPendingGate, getPendingGate, shouldBlockPendingGate, shouldBlockPendingGateBash, extractDepthVerificationMilestoneId } from "./write-gate.js";
 import { resolveManifest } from "../unit-context-manifest.js";
 import { isBlockedStateFile, isBashWriteToStateFile, BLOCKED_WRITE_ERROR } from "../write-intercept.js";
 import { loadFile, saveFile, formatContinue } from "../files.js";
@@ -432,6 +432,16 @@ export function registerHooks(pi, ecosystemHandlers) {
                     return planningGuard;
             }
         }
+        // ── Worktree-isolation write gate (#5199) ────────────────────────────
+        // Block planning-write tools from landing code at the project root when
+        // git.isolation=worktree but auto-mode hasn't created the milestone
+        // worktree yet. Without this, writes silently orphan outside git history.
+        if (isToolCallEventType("write", event) || isToolCallEventType("edit", event)) {
+            const wtBasePath = resolveWorktreeProjectRoot(dash.basePath ?? discussionBasePath);
+            const wtGuard = shouldBlockWorktreeWrite(event.toolName, event.input.path, wtBasePath, isAutoActive(), dash.currentUnit?.type);
+            if (wtGuard.block)
+                return wtGuard;
+        }
         // ── Single-writer engine: block direct writes to STATE.md ──────────
         // Covers write, edit, and bash tools to prevent bypass vectors.
         if (isToolCallEventType("write", event)) {