gsd-pi 2.81.0-dev.72a81bdf3 → 2.82.0-dev.2841a1e44

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

@@ -92,6 +92,7 @@ import { compileUnitToolContract } from "./tool-contract.js";
 import { createWorktreeSafetyModule } from "./worktree-safety.js";
 import { resolveManifest } from "./unit-context-manifest.js";
 import { classifyFailure } from "./recovery-classification.js";
+import { supportsStructuredQuestions } from "./workflow-mcp.js";
 import { WorktreeLifecycle, } from "./worktree-lifecycle.js";
 import { WorktreeStateProjection } from "./worktree-state-projection.js";
 import { reorderForCaching } from "./prompt-ordering.js";
@@ -711,13 +712,11 @@ export async function cleanupAfterLoopExit(ctx) {
         }
         initHealthWidget(ctx);
     }
-    // ADR-016 phase 3 (#5693): the stop-path basePath restore routes through
-    // `Lifecycle.restoreToProjectRoot()`, the sole owner of `s.basePath`
-    // mutation. The verb assigns `s.basePath` before any throwable work
-    // (rebuildGitService, cache invalidation), so a thrown error still leaves
-    // basePath restored — no fallback assignment needed at the call site.
-    // The chdir stays here because `restoreToProjectRoot` is a pure
-    // session-state mutation.
+    // ADR-016 phase 3 (#5693): the stop-path basePath restore + chdir routes
+    // through `Lifecycle.restoreToProjectRoot()`, the sole owner of both
+    // `s.basePath` mutation and the paired `process.chdir` for auto-loop
+    // transitions. The verb assigns `s.basePath` before any throwable work, so
+    // a thrown error still leaves basePath restored.
     if (s.originalBasePath) {
         try {
             buildLifecycle().restoreToProjectRoot();
@@ -725,12 +724,6 @@ export async function cleanupAfterLoopExit(ctx) {
         catch (err) {
             logWarning("engine", `restore project root failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
         }
-        try {
-            process.chdir(s.originalBasePath);
-        }
-        catch (err) {
-            logWarning("engine", `basePath restore/chdir failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
-        }
     }
     if (s.originalBasePath && s.cmdCtx) {
         const result = await rerootCommandSession(s.cmdCtx, s.originalBasePath);
@@ -1001,8 +994,8 @@ export async function stopAuto(ctx, pi, reason, options = {}) {
             }
         }
         // ── Step 7: Restore basePath and chdir (ADR-016 phase 3, #5693) ──
-        // `restoreToProjectRoot` assigns s.basePath before any throwable work;
-        // no fallback assignment is needed at the call site.
+        // `restoreToProjectRoot` owns both s.basePath restore and process.chdir;
+        // no paired chdir is needed at the call site.
         if (s.originalBasePath) {
             try {
                 buildLifecycle().restoreToProjectRoot();
@@ -1010,13 +1003,6 @@ export async function stopAuto(ctx, pi, reason, options = {}) {
             catch (e) {
                 debugLog("stop-cleanup-basepath", { error: e instanceof Error ? e.message : String(e) });
             }
-            try {
-                process.chdir(s.basePath);
-            }
-            catch (err) {
-                /* best-effort */
-                logWarning("engine", `chdir failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
-            }
         }
         // Re-root the active command session/tool runtime after worktree teardown.
         // mergeAndExit restores process.cwd(), but AgentSession has already captured
@@ -1385,6 +1371,66 @@ export function buildWorktreeLifecycleDeps() {
 function buildLifecycle() {
     return new WorktreeLifecycle(s, buildWorktreeLifecycleDeps());
 }
+/**
+ * Build the production `DispatchAdapter` used by `createWiredAutoOrchestrationModule`.
+ *
+ * Exported so tests can verify parity with `runDispatch`'s `resolveDispatch` call —
+ * the wired adapter must derive `structuredQuestionsAvailable`, `sessionContextWindow`,
+ * `sessionProvider`, and `modelRegistry` the same way phases.ts:runDispatch does.
+ */
+export function createWiredDispatchAdapter(ctx, pi, dispatchBasePath) {
+    return {
+        async decideNextUnit(input) {
+            const state = input.stateSnapshot;
+            const active = state.activeMilestone;
+            if (!active)
+                return null;
+            const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
+            // Derive session-derived dispatch inputs the same way phases.ts:runDispatch does
+            // (#5789). Prefer caller-supplied values when present so test harnesses and
+            // alternative wirings can inject deterministic snapshots; otherwise pull from
+            // the captured pi/ctx references.
+            const sessionProvider = input.sessionProvider ?? ctx.model?.provider;
+            const sessionContextWindow = input.sessionContextWindow ?? ctx.model?.contextWindow;
+            const modelRegistry = input.modelRegistry ?? ctx.modelRegistry;
+            const authMode = sessionProvider && typeof ctx.modelRegistry?.getProviderAuthMode === "function"
+                ? ctx.modelRegistry.getProviderAuthMode(sessionProvider)
+                : undefined;
+            const activeTools = typeof pi.getActiveTools === "function" ? pi.getActiveTools() : [];
+            // Mirrors runDispatch: deep-planning keeps approval gates in plain chat
+            // because structured questions can be cancelled outside the chat turn on
+            // some transports.
+            const structuredQuestionsAvailable = input.structuredQuestionsAvailable ??
+                (prefs?.planning_depth === "deep"
+                    ? "false"
+                    : supportsStructuredQuestions(activeTools, {
+                        authMode,
+                        baseUrl: ctx.model?.baseUrl,
+                    })
+                        ? "true"
+                        : "false");
+            const action = await resolveDispatch({
+                basePath: dispatchBasePath,
+                mid: active.id,
+                midTitle: active.title,
+                state,
+                prefs,
+                structuredQuestionsAvailable,
+                sessionContextWindow,
+                sessionProvider,
+                modelRegistry,
+            });
+            if (action.action !== "dispatch")
+                return null;
+            return {
+                unitType: action.unitType,
+                unitId: action.unitId,
+                reason: action.matchedRule ?? "dispatch",
+                preconditions: [],
+            };
+        },
+    };
+}
 /**
  * Thin entry glue for the new Auto Orchestration module.
  *
@@ -1392,7 +1438,7 @@ function buildLifecycle() {
  * no behavior changes to the existing auto loop. It provides a concrete seam
  * the next refactor steps can adopt incrementally.
  */
-export function createWiredAutoOrchestrationModule(ctx, _pi, dispatchBasePath, runtimeBasePath = resolveProjectRoot(dispatchBasePath)) {
+export function createWiredAutoOrchestrationModule(ctx, pi, dispatchBasePath, runtimeBasePath = resolveProjectRoot(dispatchBasePath)) {
     const flowId = `auto-orchestrator-${Date.now()}`;
     let seq = 0;
     const deps = {
@@ -1416,30 +1462,7 @@ export function createWiredAutoOrchestrationModule(ctx, _pi, dispatchBasePath, r
                 };
             },
         },
-        dispatch: {
-            async decideNextUnit(input) {
-                const state = input.stateSnapshot;
-                const active = state.activeMilestone;
-                if (!active)
-                    return null;
-                const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
-                const action = await resolveDispatch({
-                    basePath: dispatchBasePath,
-                    mid: active.id,
-                    midTitle: active.title,
-                    state,
-                    prefs,
-                });
-                if (action.action !== "dispatch")
-                    return null;
-                return {
-                    unitType: action.unitType,
-                    unitId: action.unitId,
-                    reason: action.matchedRule ?? "dispatch",
-                    preconditions: [],
-                };
-            },
-        },
+        dispatch: createWiredDispatchAdapter(ctx, pi, dispatchBasePath),
         recovery: {
             async classifyAndRecover(input) {
                 const recovery = classifyFailure(input);
@@ -1488,12 +1511,26 @@ export function createWiredAutoOrchestrationModule(ctx, _pi, dispatchBasePath, r
             async cleanupOnStop() { },
         },
         health: {
+            checkResourcesStale() {
+                return checkResourcesStale(s.resourceVersionOnStart);
+            },
             async preAdvanceGate() {
-                const gate = await preDispatchHealthGate(dispatchBasePath);
-                return {
-                    allow: gate.proceed,
-                    reason: gate.reason,
-                };
+                try {
+                    const gate = await preDispatchHealthGate(dispatchBasePath);
+                    if (gate.proceed) {
+                        return {
+                            kind: "pass",
+                            fixesApplied: gate.fixesApplied,
+                        };
+                    }
+                    return {
+                        kind: "fail",
+                        reason: gate.reason ?? "Pre-dispatch health check failed — run /gsd doctor for details.",
+                    };
+                }
+                catch (error) {
+                    return { kind: "threw", error };
+                }
             },
             async postAdvanceRecord(result) {
                 if (result.kind === "error") {
@@ -1561,6 +1598,45 @@ export function createWiredAutoOrchestrationModule(ctx, _pi, dispatchBasePath, r
                 }
             },
         },
+        uokGate: {
+            async emit(input) {
+                const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
+                const uokFlags = resolveUokFlags(prefs);
+                if (!uokFlags.gates)
+                    return;
+                const milestoneId = input.milestoneId ?? s.currentMilestoneId ?? undefined;
+                try {
+                    const { UokGateRunner } = await import("./uok/gate-runner.js");
+                    const runner = new UokGateRunner();
+                    runner.register({
+                        id: input.gateId,
+                        type: input.gateType,
+                        execute: async () => ({
+                            outcome: input.outcome,
+                            failureClass: input.failureClass,
+                            rationale: input.rationale,
+                            findings: input.findings ?? "",
+                        }),
+                    });
+                    await runner.run(input.gateId, {
+                        basePath: dispatchBasePath,
+                        traceId: `pre-dispatch:${flowId}`,
+                        turnId: `orch-${seq}`,
+                        milestoneId,
+                        unitType: "pre-dispatch",
+                        unitId: `orch-${seq}`,
+                    });
+                }
+                catch (err) {
+                    logWarning("engine", `uok gate emit failed: ${getErrorMessage(err)}`, {
+                        file: "auto.ts",
+                        gateId: input.gateId,
+                        gateType: input.gateType,
+                        ...(milestoneId ? { milestoneId } : {}),
+                    });
+                }
+            },
+        },
     };
     return createAutoOrchestrator(deps);
 }

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

@@ -355,6 +355,9 @@ async function writeContextModeCompactionSnapshot(basePath) {
     }
 }
 export function registerHooks(pi, ecosystemHandlers) {
+    // ADR-005 Phase 3b: surface pi-ai ProviderSwitchReport via audit, notification, and counter.
+    // Idempotent — only the first registerHooks call installs.
+    void import("../provider-switch-observer.js").then((m) => m.installProviderSwitchObserver());
     pi.on("session_start", async (_event, ctx) => {
         const basePath = contextBasePath(ctx);
         initSessionNotifications(ctx);
@@ -411,6 +414,8 @@ export function registerHooks(pi, ecosystemHandlers) {
         }
         await loadToolApiKeysForSession();
         if (!isAutoActive()) {
+            ctx.ui.setWidget("gsd-progress", undefined);
+            ctx.ui.setWidget("gsd-outcome", undefined);
             const { initHealthWidget } = await import("../health-widget.js");
             initHealthWidget(ctx);
         }

package/dist/resources/extensions/gsd/bootstrap/subagent-input.js

@@ -1,22 +1,31 @@
 export function extractSubagentAgentClasses(input) {
     if (!input || typeof input !== "object")
         return [];
-    const record = input;
     const agentClasses = [];
+    const visited = new WeakSet();
     const addAgentClass = (value) => {
         if (typeof value === "string" && value.trim().length > 0)
             agentClasses.push(value.trim());
     };
-    const addFromItems = (value) => {
+    const visitItems = (value) => {
         if (!Array.isArray(value))
             return;
         for (const item of value) {
-            if (item && typeof item === "object")
-                addAgentClass(item.agent);
+            visit(item);
         }
     };
-    addAgentClass(record.agent);
-    addFromItems(record.tasks);
-    addFromItems(record.chain);
+    const visit = (value) => {
+        if (!value || typeof value !== "object")
+            return;
+        if (visited.has(value))
+            return;
+        visited.add(value);
+        const record = value;
+        addAgentClass(record.agent);
+        visitItems(record.tasks);
+        visitItems(record.chain);
+        visitItems(record.parallel);
+    };
+    visit(input);
     return agentClasses;
 }

package/dist/resources/extensions/gsd/bootstrap/system-context.js

@@ -10,6 +10,7 @@ import { resolveAllSkillReferences, renderPreferencesForSystemPrompt, loadEffect
 import { resolveModelWithFallbacksForUnit } from "../preferences-models.js";
 import { resolveSkillReference } from "../preferences-skills.js";
 import { resolveGsdRootFile, resolveSliceFile, resolveSlicePath, resolveTaskFile, resolveTaskFiles, resolveTasksDir, relSliceFile, relSlicePath, relTaskFile } from "../paths.js";
+import { extractIntroAndRules } from "../knowledge-parser.js";
 import { ensureCodebaseMapFresh, readCodebaseMap } from "../codebase-generator.js";
 import { hasSkillSnapshot, detectNewSkills, formatSkillsXml } from "../skill-discovery.js";
 import { getActiveAutoWorktreeContext } from "../auto-worktree.js";
@@ -116,19 +117,19 @@ export async function buildBeforeAgentStartResult(event, ctx) {
     catch (e) {
         logWarning("bootstrap", `cmux prompt setup skipped: ${e.message}`);
     }
+    const ctxProjectRoot = ctx.projectRoot;
+    const basePath = typeof ctxProjectRoot === "string" && ctxProjectRoot.length > 0
+        ? ctxProjectRoot
+        : process.cwd();
     let preferenceBlock = "";
     if (loadedPreferences) {
-        const cwd = process.cwd();
+        const cwd = basePath;
         const report = resolveAllSkillReferences(loadedPreferences.preferences, cwd);
         preferenceBlock = `\n\n${renderPreferencesForSystemPrompt(loadedPreferences.preferences, report.resolutions)}`;
         if (report.warnings.length > 0) {
             ctx.ui.notify(`GSD skill preferences: ${report.warnings.length} unresolved skill${report.warnings.length === 1 ? "" : "s"}: ${report.warnings.join(", ")}`, "warning");
         }
     }
-    const { block: knowledgeBlock, globalSizeKb } = loadKnowledgeBlock(gsdHome(), process.cwd());
-    if (globalSizeKb > 4) {
-        ctx.ui.notify(`GSD: ~/.gsd/agent/KNOWLEDGE.md is ${globalSizeKb.toFixed(1)}KB — consider trimming to keep system prompt lean.`, "warning");
-    }
     // ADR-013 step 5: opportunistic decisions->memories backfill. Idempotent
     // and best-effort — first run absorbs the existing decisions table into
     // the memory store; subsequent runs are a single sentinel SELECT.
@@ -136,12 +137,47 @@ export async function buildBeforeAgentStartResult(event, ctx) {
         const { backfillDecisionsToMemories } = await import("../memory-backfill.js");
         const written = backfillDecisionsToMemories();
         if (written > 0) {
-            ctx.ui.notify(`GSD: backfilled ${written} decision${written === 1 ? "" : "s"} into the memory store (ADR-013).`, "info");
+            ctx.ui.notify(`GSD: backfilled ${written} decision${written === 1 ? "" : "s"} into the memory store.`, "info");
         }
     }
     catch (e) {
         logWarning("bootstrap", `decisions backfill failed: ${e.message}`);
     }
+    // ADR-013 Stage 2b: KNOWLEDGE.md Patterns + Lessons backfill, then
+    // re-render the hybrid projection (manual Rules + projected Patterns +
+    // projected Lessons). Both are idempotent and best-effort — failures here
+    // can't block agent startup.
+    try {
+        const { backfillKnowledgeToMemories } = await import("../knowledge-backfill.js");
+        const writtenK = backfillKnowledgeToMemories(basePath);
+        if (writtenK > 0) {
+            ctx.ui.notify(`GSD: backfilled ${writtenK} KNOWLEDGE.md row${writtenK === 1 ? "" : "s"} into the memory store.`, "info");
+        }
+    }
+    catch (e) {
+        logWarning("bootstrap", `KNOWLEDGE.md backfill failed: ${e.message}`);
+    }
+    try {
+        const { renderKnowledgeProjection } = await import("../knowledge-projection.js");
+        renderKnowledgeProjection(basePath);
+    }
+    catch (e) {
+        logWarning("bootstrap", `KNOWLEDGE.md projection render failed: ${e.message}`);
+    }
+    // ADR-013 step 6 preflight: warn when decisions / KNOWLEDGE.md rows are not
+    // yet in the memories table. Read-only; never throws. Runs after the two
+    // backfills above so the gap report reflects post-backfill state.
+    try {
+        const { reportConsolidationGaps } = await import("../memory-consolidation-scanner.js");
+        reportConsolidationGaps(basePath);
+    }
+    catch (e) {
+        logWarning("bootstrap", `memory consolidation scan failed: ${e.message}`);
+    }
+    const { block: knowledgeBlock, globalSizeKb } = loadKnowledgeBlock(gsdHome(), basePath);
+    if (globalSizeKb > 4) {
+        ctx.ui.notify(`GSD: ~/.gsd/agent/KNOWLEDGE.md is ${globalSizeKb.toFixed(1)}KB — consider trimming to keep system prompt lean.`, "warning");
+    }
     let newSkillsBlock = "";
     if (hasSkillSnapshot()) {
         const newSkills = detectNewSkills();
@@ -320,7 +356,9 @@ export async function loadMemoryBlock(userPrompt, opts = {}) {
     }
 }
 export function loadKnowledgeBlock(gsdHomeDir, cwd) {
-    // 1. Global knowledge (~/.gsd/agent/KNOWLEDGE.md) — cross-project, user-maintained
+    // 1. Global knowledge (~/.gsd/agent/KNOWLEDGE.md) — cross-project,
+    //    user-maintained. NOT migrated to memories (which are project-scoped),
+    //    so the full file is injected unchanged.
     let globalKnowledge = "";
     let globalSizeKb = 0;
     const globalKnowledgePath = join(gsdHomeDir, "agent", "KNOWLEDGE.md");
@@ -336,14 +374,19 @@ export function loadKnowledgeBlock(gsdHomeDir, cwd) {
             logWarning("bootstrap", `global knowledge file read failed: ${e.message}`);
         }
     }
-    // 2. Project knowledge (.gsd/KNOWLEDGE.md) — project-specific
+    // 2. Project knowledge (.gsd/KNOWLEDGE.md) — project-specific.
+    //    ADR-013 Stage 2b: Patterns and Lessons are projected from the
+    //    memories table and already reach the LLM via loadMemoryBlock. Inject
+    //    only the intro prose + `## Rules` section here to avoid duplicating
+    //    Patterns/Lessons content in the prompt. Rules stay manual per
+    //    ADR-013 line 39 and have no memory equivalent.
     let projectKnowledge = "";
     const knowledgePath = resolveGsdRootFile(cwd, "KNOWLEDGE");
     if (existsSync(knowledgePath)) {
         try {
-            const content = readFileSync(knowledgePath, "utf-8").trim();
-            if (content)
-                projectKnowledge = content;
+            const raw = readFileSync(knowledgePath, "utf-8").trim();
+            if (raw)
+                projectKnowledge = extractIntroAndRules(raw).trim();
         }
         catch (e) {
             logWarning("bootstrap", `project knowledge file read failed: ${e.message}`);
@@ -361,7 +404,7 @@ export function loadKnowledgeBlock(gsdHomeDir, cwd) {
     }
     const body = limitKnowledgeBlock(parts.join("\n\n"), getKnowledgeCharLimit());
     return {
-        block: `\n\n[KNOWLEDGE — Rules, patterns, and lessons learned]\n\n${body}`,
+        block: `\n\n[KNOWLEDGE — Rules from KNOWLEDGE.md (Patterns and Lessons reach the LLM via the memory block)]\n\n${body}`,
         globalSizeKb,
     };
 }

package/dist/resources/extensions/gsd/bootstrap/write-gate.js

@@ -3,6 +3,7 @@ import { copyFileSync, existsSync, lstatSync, mkdirSync, readFileSync, readlinkS
 import { isAbsolute, join, relative, resolve, sep } from "node:path";
 import { minimatch } from "minimatch";
 import { getIsolationMode } from "../preferences.js";
+import { compileSubagentPermissionContract } from "../unit-context-manifest.js";
 import { logWarning } from "../workflow-logger.js";
 import { isGsdWorktreePath, resolveWorktreeProjectRoot } from "../worktree-root.js";
 /**
@@ -681,7 +682,8 @@ export function shouldBlockPlanningUnit(toolName, pathOrCommand, basePath, unitT
     if (PLANNING_SUBAGENT_TOOLS.has(tool)) {
         if (policy.mode === "planning-dispatch") {
             const requested = (agentClasses ?? []).map(a => a.trim()).filter(Boolean);
-            const allowedSubagents = Array.isArray(policy.allowedSubagents) ? policy.allowedSubagents : [];
+            const dispatchContract = compileSubagentPermissionContract(policy);
+            const allowedSubagents = dispatchContract.allowedSubagents;
             const allowed = new Set(allowedSubagents);
             // When agentClasses is undefined, the caller has not been updated to extract
             // agent identities yet. Block and warn so stale callers surface in telemetry

package/dist/resources/extensions/gsd/clean-root-preflight.js

@@ -8,14 +8,153 @@
  *
  * Design constraints (from Trek-e approval):
  *  - Warn the user before stashing (no silent surprises)
- *  - git stash push / git stash pop only — no custom stash management layer
- *  - Stash/pop errors are logged but MUST NOT block the merge itself
+ *  - git stash push / git stash apply+drop for targeted restore
+ *  - Stash/apply errors are logged but MUST NOT block the merge itself
  *  - Fast-path status check — clean trees pay no extra cost
  */
 import { execFileSync } from "node:child_process";
+import { existsSync, readFileSync } from "node:fs";
+import { join } from "node:path";
 import { GIT_NO_PROMPT_ENV } from "./git-constants.js";
 import { logWarning } from "./workflow-logger.js";
 import { nativeHasChanges } from "./native-git-bridge.js";
+function gitText(basePath, args) {
+    return execFileSync("git", args, {
+        cwd: basePath,
+        stdio: ["ignore", "pipe", "pipe"],
+        encoding: "utf-8",
+        env: GIT_NO_PROMPT_ENV,
+    });
+}
+function gitBuffer(basePath, args) {
+    return execFileSync("git", args, {
+        cwd: basePath,
+        stdio: ["ignore", "pipe", "pipe"],
+        env: GIT_NO_PROMPT_ENV,
+    });
+}
+function errorText(err) {
+    if (!err || typeof err !== "object")
+        return String(err);
+    const parts = [];
+    const stderr = err.stderr;
+    const stdout = err.stdout;
+    for (const value of [stderr, stdout]) {
+        if (typeof value === "string")
+            parts.push(value);
+        else if (value instanceof Uint8Array)
+            parts.push(Buffer.from(value).toString("utf-8"));
+    }
+    parts.push(err instanceof Error ? err.message : String(err));
+    return parts.filter(Boolean).join("\n");
+}
+function parseAlreadyExistsNoCheckoutPaths(text) {
+    const paths = [];
+    for (const line of text.split(/\r?\n/)) {
+        const match = /^(.+?) already exists, no checkout$/i.exec(line.trim());
+        if (match?.[1])
+            paths.push(match[1]);
+    }
+    return [...new Set(paths)];
+}
+function readZeroDelimitedPaths(output) {
+    return output.split("\0").filter(Boolean);
+}
+function listStashUntrackedPaths(basePath, stashRef) {
+    try {
+        const output = gitText(basePath, ["ls-tree", "-r", "-z", "--name-only", `${stashRef}^3`]);
+        return readZeroDelimitedPaths(output);
+    }
+    catch {
+        return null;
+    }
+}
+function listStashTrackedPaths(basePath, stashRef) {
+    try {
+        const output = gitText(basePath, ["diff", "--name-only", "-z", `${stashRef}^1`, stashRef]);
+        return readZeroDelimitedPaths(output);
+    }
+    catch {
+        return null;
+    }
+}
+function isWorktreeClean(basePath) {
+    try {
+        return gitText(basePath, ["status", "--porcelain"]).trim() === "";
+    }
+    catch {
+        return null;
+    }
+}
+function stashBlobEqualsWorktreeFile(basePath, stashRef, path) {
+    try {
+        const worktreePath = join(basePath, path);
+        if (!existsSync(worktreePath))
+            return false;
+        const worktreeContent = readFileSync(worktreePath);
+        const stashContent = gitBuffer(basePath, ["show", `${stashRef}^3:${path}`]);
+        return Buffer.compare(worktreeContent, stashContent) === 0;
+    }
+    catch {
+        return null;
+    }
+}
+function reconcileAlreadyPresentUntrackedStash(basePath, milestoneId, stashRef, err) {
+    const text = errorText(err);
+    const collidedPaths = parseAlreadyExistsNoCheckoutPaths(text);
+    if (collidedPaths.length === 0)
+        return null;
+    const untrackedPaths = listStashUntrackedPaths(basePath, stashRef);
+    if (!untrackedPaths || untrackedPaths.length === 0)
+        return null;
+    const trackedPaths = listStashTrackedPaths(basePath, stashRef);
+    if (trackedPaths === null || trackedPaths.length > 0)
+        return null;
+    const untrackedPathSet = new Set(untrackedPaths);
+    if (!collidedPaths.every((path) => untrackedPathSet.has(path)))
+        return null;
+    if (!untrackedPaths.every((path) => existsSync(join(basePath, path))))
+        return null;
+    if (isWorktreeClean(basePath) !== true)
+        return null;
+    const blobComparisons = untrackedPaths.map((path) => stashBlobEqualsWorktreeFile(basePath, stashRef, path));
+    if (blobComparisons.some((result) => result === null))
+        return null;
+    const allIdentical = blobComparisons.every(Boolean);
+    if (allIdentical) {
+        let dropped = true;
+        try {
+            execFileSync("git", ["stash", "drop", stashRef], {
+                cwd: basePath,
+                stdio: ["ignore", "pipe", "pipe"],
+                encoding: "utf-8",
+                env: GIT_NO_PROMPT_ENV,
+            });
+        }
+        catch (err) {
+            dropped = false;
+            logWarning("preflight", `git stash drop ${stashRef} failed after identical preflight stash reconciliation: ${err instanceof Error ? err.message : String(err)}`);
+        }
+        return {
+            restored: true,
+            needsManualRecovery: false,
+            message: dropped
+                ? `Preflight stash for milestone ${milestoneId} contained files already present after merge; identical stash dropped.`
+                : `Preflight stash for milestone ${milestoneId} contained files already present after merge, but ${stashRef} could not be dropped and remains as a backup.`,
+            stashRef,
+            resolution: dropped ? "already-present-dropped" : "already-present-preserved",
+            collidedPaths,
+        };
+    }
+    return {
+        restored: false,
+        needsManualRecovery: false,
+        message: `Preflight stash for milestone ${milestoneId} contained untracked files already present after merge. Keeping merged files and preserving ${stashRef} as a backup.`,
+        stashRef,
+        resolution: "already-present-preserved",
+        collidedPaths,
+    };
+}
 function findPreflightStashRef(basePath, milestoneId, stashMarker) {
     const markerPrefix = `gsd-preflight-stash:${milestoneId}:`;
     let fallbackRef = null;
@@ -115,28 +254,50 @@ export function postflightPopStash(basePath, milestoneId, stashMarker, notify) {
                 message: msg,
             };
         }
-        execFileSync("git", ["stash", "pop", stashRef], {
+        execFileSync("git", ["stash", "apply", stashRef], {
             cwd: basePath,
             stdio: ["ignore", "pipe", "pipe"],
             encoding: "utf-8",
             env: GIT_NO_PROMPT_ENV,
         });
+        let dropWarning = null;
+        try {
+            execFileSync("git", ["stash", "drop", stashRef], {
+                cwd: basePath,
+                stdio: ["ignore", "pipe", "pipe"],
+                encoding: "utf-8",
+                env: GIT_NO_PROMPT_ENV,
+            });
+        }
+        catch (err) {
+            dropWarning = ` Stash was restored, but git stash drop ${stashRef} failed: ${err instanceof Error ? err.message : String(err)}.`;
+            logWarning("preflight", dropWarning.trim());
+        }
         const msg = `Restored stashed changes after milestone ${milestoneId} merge.`;
-        notify(msg, "info");
+        notify(`${msg}${dropWarning ?? ""}`, dropWarning ? "warning" : "info");
         return {
             restored: true,
             needsManualRecovery: false,
-            message: msg,
+            message: `${msg}${dropWarning ?? ""}`,
             stashRef,
+            resolution: "applied",
         };
     }
     catch (err) {
-        // Pop conflicts mean the merged code collides with the stashed changes.
+        if (stashRef) {
+            const reconciled = reconcileAlreadyPresentUntrackedStash(basePath, milestoneId, stashRef, err);
+            if (reconciled) {
+                logWarning("preflight", reconciled.message);
+                notify(reconciled.message, reconciled.resolution === "already-present-preserved" ? "warning" : "info");
+                return reconciled;
+            }
+        }
+        // Apply conflicts mean the merged code collides with the stashed changes.
         // Log a warning — the user needs to resolve manually, but the merge succeeded.
         const restoreHint = stashRef
-            ? `Run "git stash pop ${stashRef}" or "git stash apply ${stashRef}" manually to restore the correct stash.`
+            ? `Run "git stash apply ${stashRef}" manually to restore the correct stash, then "git stash drop ${stashRef}" after recovery.`
             : `Run "git stash list" to find the matching GSD preflight stash before restoring manually.`;
-        const msg = `git stash pop ${stashRef ?? ""}`.trim() + ` failed after merge of milestone ${milestoneId}: ${err instanceof Error ? err.message : String(err)}. ${restoreHint}`;
+        const msg = `git stash apply ${stashRef ?? ""}`.trim() + ` failed after merge of milestone ${milestoneId}: ${err instanceof Error ? err.message : String(err)}. ${restoreHint}`;
         logWarning("preflight", msg);
         notify(msg, "warning");
         return {
@@ -144,6 +305,7 @@ export function postflightPopStash(basePath, milestoneId, stashMarker, notify) {
             needsManualRecovery: true,
             message: msg,
             ...(stashRef ? { stashRef } : {}),
+            resolution: "manual-recovery",
         };
     }
 }