gsd-pi 2.76.0-dev.b072ebb73 → 2.76.0-dev.fe143342a

package/scripts/link-workspace-packages.cjs

@@ -34,6 +34,7 @@ const packageMap = {
   'pi-coding-agent': { scope: '@gsd', name: 'pi-coding-agent' },
   'pi-tui': { scope: '@gsd', name: 'pi-tui' },
   'rpc-client': { scope: '@gsd-build', name: 'rpc-client' },
+  'mcp-server': { scope: '@gsd-build', name: 'mcp-server' },
 }
 
 for (const scopeDir of Object.values(scopeDirs)) {

package/src/resources/extensions/claude-code-cli/stream-adapter.ts

@@ -867,6 +867,69 @@ function normalizeToolResultContent(content: unknown): ExternalToolResultContent
 	return blocks.length > 0 ? blocks : [{ type: "text", text: "" }];
 }
 
+/**
+ * Extract a `details` payload from an MCP tool-result block.
+ *
+ * MCP's `CallToolResult` carries structured data in `structuredContent` — the
+ * protocol's supported channel for non-text payloads. Claude Code's synthetic
+ * user message may surface that field in one of two shapes depending on SDK
+ * version: as a sibling on the `mcp_tool_result` block itself, or as a
+ * dedicated content sub-block with `type: "structuredContent"`. Snake-case
+ * (`structured_content`) is accepted defensively in case a transport hop
+ * rewrites casing. All other shapes fall back to an empty object so callers
+ * can rely on `details` being present.
+ */
+function extractStructuredDetailsFromBlock(block: Record<string, unknown>): Record<string, unknown> | undefined {
+	const sibling = block.structuredContent ?? (block as Record<string, unknown>).structured_content;
+	if (sibling && typeof sibling === "object" && !Array.isArray(sibling)) {
+		return sibling as Record<string, unknown>;
+	}
+
+	if (Array.isArray(block.content)) {
+		for (const item of block.content) {
+			if (!item || typeof item !== "object") continue;
+			const sub = item as Record<string, unknown>;
+			if (sub.type !== "structuredContent" && sub.type !== "structured_content") continue;
+			const payload = sub.structuredContent ?? sub.structured_content ?? sub.data ?? sub.value;
+			if (payload && typeof payload === "object" && !Array.isArray(payload)) {
+				return payload as Record<string, unknown>;
+			}
+		}
+	}
+
+	// Return undefined (not {}) when no structured payload is present, matching
+	// the pre-#4477 contract where `details` was nullable. An empty-object
+	// sentinel is truthy and breaks downstream consumers that gate on
+	// `if (details)`. `undefined` matches the type of the field these results
+	// flow into (`Record<string, unknown> | undefined`).
+	return undefined;
+}
+
+/**
+ * True for items that are MCP `structuredContent` pseudo-blocks living inside
+ * a tool-result `content[]` array. These blocks carry the structured payload
+ * (extracted separately by `extractStructuredDetailsFromBlock`) and must NOT
+ * leak into the visible content rendered to the user — otherwise the renderer
+ * stringifies the JSON pseudo-block and shows it next to the actual tool
+ * output. See PR #4477 review (CodeRabbit, post-fix-round).
+ */
+function isStructuredContentPseudoBlock(item: unknown): boolean {
+	if (!item || typeof item !== "object") return false;
+	const type = (item as Record<string, unknown>).type;
+	return type === "structuredContent" || type === "structured_content";
+}
+
+/**
+ * Strip `structuredContent` pseudo-blocks from a tool-result content array
+ * before normalization. The structured payload is extracted via the sibling
+ * `structuredContent` field (or a dedicated extractor pass on the raw block);
+ * the visible content path must not include the pseudo-block itself.
+ */
+function stripStructuredContentPseudoBlocks(content: unknown): unknown {
+	if (!Array.isArray(content)) return content;
+	return content.filter((item) => !isStructuredContentPseudoBlock(item));
+}
+
 /** Extract tool result payloads from an SDK synthetic user message, keyed by tool-use ID. */
 export function extractToolResultsFromSdkUserMessage(message: SDKUserMessage): Array<{
 	toolUseId: string;
@@ -890,8 +953,8 @@ export function extractToolResultsFromSdkUserMessage(message: SDKUserMessage): A
 		extracted.push({
 			toolUseId,
 			result: {
-				content: normalizeToolResultContent(block.content),
-				details: {},
+				content: normalizeToolResultContent(stripStructuredContentPseudoBlocks(block.content)),
+				details: extractStructuredDetailsFromBlock(block),
 				isError: block.is_error === true,
 			},
 		});
@@ -906,8 +969,8 @@ export function extractToolResultsFromSdkUserMessage(message: SDKUserMessage): A
 				extracted.push({
 					toolUseId,
 					result: {
-						content: normalizeToolResultContent(toolResult.content),
-						details: {},
+						content: normalizeToolResultContent(stripStructuredContentPseudoBlocks(toolResult.content)),
+						details: extractStructuredDetailsFromBlock(toolResult),
 						isError: toolResult.is_error === true,
 					},
 				});

package/src/resources/extensions/claude-code-cli/tests/stream-adapter.test.ts

@@ -372,13 +372,146 @@ describe("stream-adapter — Claude Code external tool results", () => {
 				toolUseId: "tool-bash-1",
 				result: {
 					content: [{ type: "text", text: "line 1\nline 2" }],
-					details: {},
+					// extractStructuredDetailsFromBlock returns undefined when no
+					// structured payload exists, restoring the pre-#4477 nullable
+					// contract (#4477 review feedback).
+					details: undefined,
 					isError: false,
 				},
 			},
 		]);
 	});
 
+	test("extractToolResultsFromSdkUserMessage reads structuredContent as a sibling field (#4472)", () => {
+		const message: SDKUserMessage = {
+			type: "user",
+			session_id: "sess-1",
+			parent_tool_use_id: "tool-mcp-1",
+			message: {
+				role: "user",
+				content: [
+					{
+						type: "mcp_tool_result",
+						tool_use_id: "tool-mcp-1",
+						content: [{ type: "text", text: "Gate Q3 result saved: verdict=pass" }],
+						is_error: false,
+						structuredContent: { gateId: "Q3", verdict: "pass" },
+					} as unknown as Record<string, unknown>,
+				],
+			},
+		};
+
+		const results = extractToolResultsFromSdkUserMessage(message);
+		assert.deepEqual(results[0].result.details, { gateId: "Q3", verdict: "pass" });
+	});
+
+	test("extractToolResultsFromSdkUserMessage reads structuredContent from a content sub-block (#4472)", () => {
+		const message: SDKUserMessage = {
+			type: "user",
+			session_id: "sess-1",
+			parent_tool_use_id: "tool-mcp-2",
+			message: {
+				role: "user",
+				content: [
+					{
+						type: "mcp_tool_result",
+						tool_use_id: "tool-mcp-2",
+						content: [
+							{ type: "text", text: "Gate Q4 result saved: verdict=flag" },
+							{ type: "structuredContent", structuredContent: { gateId: "Q4", verdict: "flag" } },
+						],
+						is_error: false,
+					} as unknown as Record<string, unknown>,
+				],
+			},
+		};
+
+		const results = extractToolResultsFromSdkUserMessage(message);
+		assert.deepEqual(results[0].result.details, { gateId: "Q4", verdict: "flag" });
+	});
+
+	test("#4477 extractToolResultsFromSdkUserMessage does NOT leak structuredContent pseudo-blocks into visible content", () => {
+		// Regression: when a content sub-block carries `type: "structuredContent"`,
+		// it carries the structured payload (extracted separately into `details`)
+		// and must NOT appear in the visible `content` array — otherwise the
+		// renderer stringifies the JSON pseudo-block and shows it next to the
+		// actual tool output. See PR #4477 review (CodeRabbit, post-fix-round).
+		const message: SDKUserMessage = {
+			type: "user",
+			session_id: "sess-1",
+			parent_tool_use_id: "tool-mcp-strip",
+			message: {
+				role: "user",
+				content: [
+					{
+						type: "mcp_tool_result",
+						tool_use_id: "tool-mcp-strip",
+						content: [
+							{ type: "text", text: "Gate Q5 result saved: verdict=pass" },
+							{ type: "structuredContent", structuredContent: { gateId: "Q5", verdict: "pass" } },
+							{ type: "text", text: "second visible line" },
+							// snake_case variant — also a pseudo-block; also must be stripped
+							{ type: "structured_content", structured_content: { extra: "data" } },
+						],
+						is_error: false,
+					} as unknown as Record<string, unknown>,
+				],
+			},
+		};
+
+		const results = extractToolResultsFromSdkUserMessage(message);
+		assert.equal(results.length, 1, "should extract one result");
+		const result = results[0].result;
+
+		// The structured payload IS extracted to `details`.
+		assert.deepEqual(result.details, { gateId: "Q5", verdict: "pass" });
+
+		// The visible content has the two text blocks but NEITHER pseudo-block.
+		const visibleTexts = result.content.map((c: any) => c.text);
+		assert.deepEqual(
+			visibleTexts,
+			["Gate Q5 result saved: verdict=pass", "second visible line"],
+			"visible content must include only the two text blocks; both structuredContent variants must be stripped",
+		);
+
+		// Belt-and-suspenders: assert no rendered text shows the JSON serialization
+		// of a pseudo-block. We don't check for bare keys like "gateId" or "verdict"
+		// because those are legitimate words in the gate-result message text. The
+		// regression signature would be a JSON-shaped substring that could only
+		// appear via stringification.
+		const allText = visibleTexts.join("\n");
+		assert.ok(
+			!allText.includes('"structuredContent"'),
+			"rendered content must not include the pseudo-block type marker as JSON text",
+		);
+		assert.ok(
+			!allText.includes('"structured_content"'),
+			"rendered content must not include the snake_case pseudo-block type marker as JSON text",
+		);
+	});
+
+	test("extractToolResultsFromSdkUserMessage accepts snake_case structured_content defensively (#4472)", () => {
+		const message: SDKUserMessage = {
+			type: "user",
+			session_id: "sess-1",
+			parent_tool_use_id: "tool-mcp-3",
+			message: {
+				role: "user",
+				content: [
+					{
+						type: "mcp_tool_result",
+						tool_use_id: "tool-mcp-3",
+						content: [{ type: "text", text: "ok" }],
+						structured_content: { operation: "save_gate_result" },
+					} as unknown as Record<string, unknown>,
+				],
+			},
+		};
+
+		const results = extractToolResultsFromSdkUserMessage(message);
+		assert.deepEqual(results[0].result.details, { operation: "save_gate_result" });
+	});
+
 	test("extractToolResultsFromSdkUserMessage falls back to tool_use_result", () => {
 		const message: SDKUserMessage = {
 			type: "user",
@@ -398,7 +531,9 @@ describe("stream-adapter — Claude Code external tool results", () => {
 				toolUseId: "tool-read-1",
 				result: {
 					content: [{ type: "text", text: "file contents" }],
-					details: {},
+					// undefined (not {}) per the restored nullable contract — see
+					// the analogous assertion in the tool_result test above.
+					details: undefined,
 					isError: true,
 				},
 			},

package/src/resources/extensions/gsd/auto/loop-deps.ts

@@ -213,6 +213,7 @@ export interface LoopDeps {
     retryContext?: { isRetry: boolean; previousTier?: string },
     isAutoMode?: boolean,
     sessionModelOverride?: { provider: string; id: string } | null,
+    autoModeStartThinkingLevel?: ReturnType<ExtensionAPI["getThinkingLevel"]> | null,
   ) => Promise<{
     routing: { tier: string; modelDowngraded: boolean } | null;
     appliedModel: { provider: string; id: string } | null;

package/src/resources/extensions/gsd/auto/phases.ts

@@ -1471,6 +1471,7 @@ export async function runUnitPhase(
     sidecarItem ? undefined : { isRetry, previousTier },
     undefined,
     s.manualSessionModelOverride,
+    s.autoModeStartThinkingLevel,
   );
   s.currentUnitRouting =
     modelResult.routing as AutoSession["currentUnitRouting"];
@@ -1485,6 +1486,9 @@ export async function runUnitPhase(
     if (match) {
       const ok = await pi.setModel(match, { persist: false });
       if (ok) {
+        if (s.autoModeStartThinkingLevel) {
+          pi.setThinkingLevel(s.autoModeStartThinkingLevel);
+        }
         s.currentUnitModel = match as AutoSession["currentUnitModel"];
         ctx.ui.notify(`Hook model override: ${match.provider}/${match.id}`, "info");
       } else {

package/src/resources/extensions/gsd/auto/session.ts

@@ -17,7 +17,7 @@
  */
 
 import type { Api, Model } from "@gsd/pi-ai";
-import type { ExtensionCommandContext } from "@gsd/pi-coding-agent";
+import type { ExtensionAPI, ExtensionCommandContext } from "@gsd/pi-coding-agent";
 import type { GitServiceImpl } from "../git-service.js";
 import type { CaptureEntry } from "../captures.js";
 import type { BudgetAlertLevel } from "../auto-budget.js";
@@ -40,6 +40,8 @@ export interface StartModel {
   id: string;
 }
 
+export type ThinkingLevelSnapshot = ReturnType<ExtensionAPI["getThinkingLevel"]>;
+
 export interface PendingVerificationRetry {
   unitId: string;
   failureContext: string;
@@ -120,6 +122,8 @@ export class AutoSession {
   currentDispatchedModelId: string | null = null;
   originalModelId: string | null = null;
   originalModelProvider: string | null = null;
+  autoModeStartThinkingLevel: ThinkingLevelSnapshot | null = null;
+  originalThinkingLevel: ThinkingLevelSnapshot | null = null;
   lastBudgetAlertLevel: BudgetAlertLevel = 0;
 
   // ── Recovery ─────────────────────────────────────────────────────────────
@@ -241,6 +245,8 @@ export class AutoSession {
     this.currentDispatchedModelId = null;
     this.originalModelId = null;
     this.originalModelProvider = null;
+    this.autoModeStartThinkingLevel = null;
+    this.originalThinkingLevel = null;
     this.lastBudgetAlertLevel = 0;
 
     // Recovery

package/src/resources/extensions/gsd/auto-model-selection.ts

@@ -18,6 +18,7 @@ import { getSessionModelOverride } from "./session-model-override.js";
 import { logWarning } from "./workflow-logger.js";
 import { resolveUokFlags } from "./uok/flags.js";
 import { applyModelPolicyFilter } from "./uok/model-policy.js";
+import { isModelBlocked } from "./blocked-models.js";
 
 export interface ModelSelectionResult {
   /** Routing metadata for metrics recording */
@@ -32,6 +33,14 @@ export interface PreferredModelConfig {
   source: "explicit" | "synthesized";
 }
 
+function reapplyThinkingLevel(
+  pi: ExtensionAPI,
+  level: ReturnType<ExtensionAPI["getThinkingLevel"]> | null | undefined,
+): void {
+  if (!level) return;
+  pi.setThinkingLevel(level);
+}
+
 export function resolvePreferredModelConfig(
   unitType: string,
   autoModeStartModel: { provider: string; id: string; flatRateCtx?: FlatRateContext } | null,
@@ -96,6 +105,8 @@ export async function selectAndApplyModel(
   isAutoMode = true,
   /** Explicit /gsd model pin captured at bootstrap for long-running auto loops. */
   sessionModelOverride?: { provider: string; id: string } | null,
+  /** Thinking level captured at auto-mode start and re-applied after model swaps. */
+  autoModeStartThinkingLevel?: ReturnType<ExtensionAPI["getThinkingLevel"]> | null,
 ): Promise<ModelSelectionResult> {
   const uokFlags = resolveUokFlags(prefs);
   const effectiveSessionModelOverride = sessionModelOverride === undefined
@@ -352,6 +363,18 @@ export async function selectAndApplyModel(
         attemptedPolicyEligible = true;
       }
 
+      // Skip models the provider has previously rejected for this account
+      // (issue #4513).  The block is persisted in .gsd/runtime/blocked-models.json
+      // so it survives /gsd auto restarts — without this, the same dead model
+      // gets reselected after every restart.
+      if (isModelBlocked(basePath, model.provider, model.id)) {
+        ctx.ui.notify(
+          `Skipping blocked model ${model.provider}/${model.id} (provider rejected it for this account).`,
+          "warning",
+        );
+        continue;
+      }
+
       // Warn if the ID is ambiguous across providers
       if (!modelId.includes("/")) {
         const providers = availableModels.filter(m => m.id === modelId).map(m => m.provider);
@@ -367,6 +390,7 @@ export async function selectAndApplyModel(
       const ok = await pi.setModel(model, { persist: false });
       if (ok) {
         appliedModel = model;
+        reapplyThinkingLevel(pi, autoModeStartThinkingLevel);
 
         // ADR-005: Adjust active tool set for the selected model's provider capabilities.
         // Hard-filter incompatible tools, then let extensions override via adjust_tool_set hook.
@@ -425,19 +449,33 @@ export async function selectAndApplyModel(
     // No model preference for this unit type — re-apply the model captured
     // at auto-mode start to prevent bleed from shared global settings.json (#650).
     const availableModels = ctx.modelRegistry.getAvailable();
-    const startModel = availableModels.find(
-      m => m.provider === autoModeStartModel.provider && m.id === autoModeStartModel.id,
-    );
-    if (startModel) {
-      const ok = await pi.setModel(startModel, { persist: false });
-      if (!ok) {
-        const byId = availableModels.find(m => m.id === autoModeStartModel.id);
-        if (byId) {
-          const fallbackOk = await pi.setModel(byId, { persist: false });
-          if (fallbackOk) appliedModel = byId;
+    const startBlocked = isModelBlocked(basePath, autoModeStartModel.provider, autoModeStartModel.id);
+    if (startBlocked) {
+      ctx.ui.notify(
+        `Auto-mode start model ${autoModeStartModel.provider}/${autoModeStartModel.id} is blocked for this account. Using current session model instead.`,
+        "warning",
+      );
+    } else {
+      const startModel = availableModels.find(
+        m => m.provider === autoModeStartModel.provider && m.id === autoModeStartModel.id,
+      );
+      if (startModel) {
+        const ok = await pi.setModel(startModel, { persist: false });
+        if (!ok) {
+          const byId = availableModels.find(
+            m => m.id === autoModeStartModel.id && !isModelBlocked(basePath, m.provider, m.id),
+          );
+          if (byId) {
+            const fallbackOk = await pi.setModel(byId, { persist: false });
+            if (fallbackOk) {
+              appliedModel = byId;
+              reapplyThinkingLevel(pi, autoModeStartThinkingLevel);
+            }
+          }
+        } else {
+          appliedModel = startModel;
+          reapplyThinkingLevel(pi, autoModeStartThinkingLevel);
         }
-      } else {
-        appliedModel = startModel;
       }
     }
   }

package/src/resources/extensions/gsd/auto-start.ts

@@ -60,7 +60,7 @@ import { initRoutingHistory } from "./routing-history.js";
 import { restoreHookState, resetHookState } from "./post-unit-hooks.js";
 import { resetProactiveHealing, setLevelChangeCallback } from "./doctor-proactive.js";
 import { snapshotSkills } from "./skill-discovery.js";
-import { isDbAvailable, getMilestone, openDatabase } from "./gsd-db.js";
+import { isDbAvailable, getMilestone, openDatabase, getDbStatus } from "./gsd-db.js";
 import { hideFooter } from "./auto-dashboard.js";
 import {
   debugLog,
@@ -92,7 +92,7 @@ import type { WorktreeResolver } from "./worktree-resolver.js";
 import { getSessionModelOverride } from "./session-model-override.js";
 
 export interface BootstrapDeps {
-  shouldUseWorktreeIsolation: () => boolean;
+  shouldUseWorktreeIsolation: (basePath?: string) => boolean;
   registerSigtermHandler: (basePath: string) => void;
   lockBase: () => string;
   buildResolver: () => WorktreeResolver;
@@ -273,8 +273,8 @@ export async function bootstrapAutoSession(
   //
   // Precedence:
   // 1) Explicit session override via /gsd model (this session)
-  // 2) GSD model preferences from PREFERENCES.md (validated against live auth)
-  // 3) Current session model from settings/session restore (if provider ready)
+  // 2) Current session model from settings/session restore (if provider ready)
+  // 3) GSD model preferences from PREFERENCES.md (validated against live auth)
   //
   // This preserves #3517 defaults while honoring explicit runtime model
   // selection for subsequent /gsd runs in the same session.
@@ -314,11 +314,14 @@ export async function bootstrapAutoSession(
   }
   const sessionModelReady =
     ctx.model && ctx.modelRegistry.isProviderRequestReady(ctx.model.provider);
+  const currentSessionModel = (sessionModelReady && ctx.model)
+    ? { provider: ctx.model.provider, id: ctx.model.id }
+    : null;
+  const startThinkingSnapshot = pi.getThinkingLevel();
   const startModelSnapshot = manualSessionOverride
+    ?? currentSessionModel
     ?? validatedPreferredModel
-    ?? (sessionModelReady && ctx.model
-      ? { provider: ctx.model.provider, id: ctx.model.id }
-      : null);
+    ?? null;
 
   try {
     // Validate GSD_PROJECT_ID early so the user gets immediate feedback
@@ -340,7 +343,7 @@ export async function bootstrapAutoSession(
     const hasLocalGit = existsSync(join(base, ".git"));
     if (!hasLocalGit || isInheritedRepo(base)) {
       const mainBranch =
-        loadEffectiveGSDPreferences()?.preferences?.git?.main_branch || "main";
+        loadEffectiveGSDPreferences(base)?.preferences?.git?.main_branch || "main";
       nativeInit(base, mainBranch);
     }
 
@@ -358,7 +361,7 @@ export async function bootstrapAutoSession(
     // Ensure .gitignore has baseline patterns.
     // ensureGitignore checks for git-tracked .gsd/ files and skips the
     // ".gsd" pattern if the project intentionally tracks .gsd/ in git.
-    const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git;
+    const gitPrefs = loadEffectiveGSDPreferences(base)?.preferences?.git;
     const manageGitignore = gitPrefs?.manage_gitignore;
     ensureGitignore(base, { manageGitignore });
     if (manageGitignore !== false) untrackRuntimeFiles(base);
@@ -387,7 +390,7 @@ export async function bootstrapAutoSession(
     // Initialize GitServiceImpl
     s.gitService = new GitServiceImpl(
       s.basePath,
-      loadEffectiveGSDPreferences()?.preferences?.git ?? {},
+      loadEffectiveGSDPreferences(base)?.preferences?.git ?? {},
     );
 
     // ── Debug mode ──
@@ -431,7 +434,7 @@ export async function bootstrapAutoSession(
     // was lost due to session ending between completion and teardown.
     // Must run after DB open and before worktree entry.
     try {
-      const auditResult = auditOrphanedMilestoneBranches(base, getIsolationMode());
+      const auditResult = auditOrphanedMilestoneBranches(base, getIsolationMode(base));
       for (const msg of auditResult.recovered) {
         ctx.ui.notify(`Orphan audit: ${msg}`, "info");
       }
@@ -451,7 +454,7 @@ export async function bootstrapAutoSession(
     // Stale worktree state recovery (#654)
     if (
       state.activeMilestone &&
-      shouldUseWorktreeIsolation() &&
+      shouldUseWorktreeIsolation(base) &&
       !detectWorktreeName(base)
     ) {
       const wtPath = getAutoWorktreePath(base, state.activeMilestone.id);
@@ -469,7 +472,7 @@ export async function bootstrapAutoSession(
     if (
       state.activeMilestone &&
       (state.phase === "pre-planning" || state.phase === "complete") &&
-      getIsolationMode() !== "none" &&
+      getIsolationMode(base) !== "none" &&
       !detectWorktreeName(base) &&
       !base.includes(`${pathSep}.gsd${pathSep}worktrees${pathSep}`)
     ) {
@@ -664,15 +667,16 @@ export async function bootstrapAutoSession(
     s.pendingQuickTasks = [];
     s.currentUnit = null;
     s.currentMilestoneId = state.activeMilestone?.id ?? null;
-    s.originalModelId = ctx.model?.id ?? null;
-    s.originalModelProvider = ctx.model?.provider ?? null;
+    s.originalModelId = startModelSnapshot?.id ?? ctx.model?.id ?? null;
+    s.originalModelProvider = startModelSnapshot?.provider ?? ctx.model?.provider ?? null;
+    s.originalThinkingLevel = startThinkingSnapshot ?? null;
 
     // Register SIGTERM handler
     registerSigtermHandler(base);
 
     // Capture integration branch
     if (s.currentMilestoneId) {
-      if (getIsolationMode() !== "none") {
+      if (getIsolationMode(base) !== "none") {
         captureIntegrationBranch(base, s.currentMilestoneId);
       }
       setActiveMilestoneId(base, s.currentMilestoneId);
@@ -681,7 +685,7 @@ export async function bootstrapAutoSession(
     // Guard against stale milestone branch when isolation:none (#3613).
     // A prior session with isolation:branch/worktree may have left HEAD on
     // milestone/<MID>. Auto-checkout back to the integration branch.
-    if (getIsolationMode() === "none" && nativeIsRepo(base)) {
+    if (getIsolationMode(base) === "none" && nativeIsRepo(base)) {
       try {
         const currentBranch = nativeGetCurrentBranch(base);
         if (currentBranch.startsWith("milestone/")) {
@@ -712,7 +716,7 @@ export async function bootstrapAutoSession(
 
     if (
       s.currentMilestoneId &&
-      getIsolationMode() !== "none" &&
+      getIsolationMode(base) !== "none" &&
       !detectWorktreeName(base) &&
       !isUnderGsdWorktrees(base)
     ) {
@@ -758,9 +762,22 @@ export async function bootstrapAutoSession(
     // call returns "db_unavailable", triggering artifact-retry which
     // re-dispatches the same task — producing an infinite loop (#2419).
     if (existsSync(gsdDbPath) && !isDbAvailable()) {
+      const dbStatus = getDbStatus();
+      const phaseHint = dbStatus.lastPhase === "open"
+        ? "The database file could not be opened"
+        : dbStatus.lastPhase === "initSchema"
+          ? "The database schema could not be initialized"
+          : dbStatus.lastPhase === "vacuum-recovery"
+            ? "Corruption recovery (VACUUM) failed"
+            : dbStatus.attempted
+              ? "The database could not be opened (phase unknown)"
+              : "The database provider could not be loaded";
+      const errorDetail = dbStatus.lastError ? ` (${dbStatus.lastError.message})` : "";
+      const providerHint = dbStatus.provider
+        ? ` Provider: ${dbStatus.provider}.`
+        : " No SQLite provider available — check Node >= 22 or install better-sqlite3.";
       ctx.ui.notify(
-        "SQLite database exists but failed to open. Auto-mode cannot proceed without a working database provider. " +
-          "Check for corrupt gsd.db or missing native SQLite bindings.",
+        `SQLite database exists but failed to open: ${gsdDbPath}. ${phaseHint}${errorDetail}.${providerHint}`,
         "error",
       );
       return releaseLockAndReturn();
@@ -779,6 +796,7 @@ export async function bootstrapAutoSession(
         id: startModelSnapshot.id,
       };
     }
+    s.autoModeStartThinkingLevel = startThinkingSnapshot ?? null;
     s.manualSessionModelOverride = manualSessionOverride ?? null;
 
     // Apply worker model override from parallel orchestrator (#worker-model).
@@ -801,7 +819,7 @@ export async function bootstrapAutoSession(
     }
 
     // Snapshot installed skills
-    if (resolveSkillDiscoveryMode() !== "off") {
+    if (resolveSkillDiscoveryMode(base) !== "off") {
       snapshotSkills();
     }
 
@@ -835,7 +853,7 @@ export async function bootstrapAutoSession(
     // FlatRateContext used by selectAndApplyModel so user-declared
     // flat-rate providers and externalCli auto-detection are respected.
     const { isFlatRateProvider, buildFlatRateContext } = await import("./auto-model-selection.js");
-    const bannerPrefs = loadEffectiveGSDPreferences()?.preferences;
+    const bannerPrefs = loadEffectiveGSDPreferences(base)?.preferences;
     const effectiveProvider = s.autoModeStartModel?.provider ?? ctx.model?.provider;
     const effectivelyEnabled = routingConfig.enabled
       && (routingConfig.allow_flat_rate_providers