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

package/dist/mcp-server.d.ts

@@ -1,6 +1,11 @@
 /**
  * Minimal tool interface matching GSD's AgentTool shape.
  * Avoids a direct dependency on @gsd/pi-agent-core from this compiled module.
+ *
+ * `details` and `isError` are optional fields that runtime tool implementations
+ * may populate. The MCP transport drops non-standard fields, so the wrapper at
+ * the call site mirrors `details` into `structuredContent` and forwards
+ * `isError` directly. See #4472.
  */
 export interface McpToolDef {
     name: string;
@@ -13,6 +18,8 @@ export interface McpToolDef {
             data?: string;
             mimeType?: string;
         }>;
+        details?: Record<string, unknown>;
+        isError?: boolean;
     }>;
 }
 /**

package/dist/mcp-server.js

@@ -1,3 +1,21 @@
+/**
+ * Strict plain-object guard. True only for object literals and
+ * `Object.create(null)` — not for `Date`, `URL`, `Map`, `Set`, class instances,
+ * or arrays. Used to gate `structuredContent` forwarding so the MCP transport
+ * receives only true JSON objects (the protocol contract). See #4477 review.
+ *
+ * Mirrored in `packages/mcp-server/src/workflow-tools.ts` for the
+ * `adaptExecutorResult` adapter on the workflow path. Keep both copies in
+ * sync if the contract definition needs to evolve.
+ */
+function isPlainObject(value) {
+    if (value === null || typeof value !== 'object')
+        return false;
+    if (Array.isArray(value))
+        return false;
+    const proto = Object.getPrototypeOf(value);
+    return proto === null || proto === Object.prototype;
+}
 // MCP SDK subpath imports use wildcard exports (./*) in @modelcontextprotocol/sdk's
 // package.json export map. The wildcard maps "./foo" → "./dist/cjs/foo" (no .js
 // suffix), so bare subpath specifiers like `${MCP_PKG}/server/stdio` resolve to
@@ -83,7 +101,23 @@ export async function startMcpServer(options) {
                 // by stringifying into a text block so clients see the payload.
                 return { type: 'text', text: JSON.stringify(block) };
             });
-            return { content };
+            // Forward a tool's runtime `details` field to MCP's `structuredContent`
+            // channel. The protocol drops non-standard fields on the wire, so tools
+            // that populate `details` for client-side renderers (e.g. save_gate_result)
+            // would otherwise arrive empty on the other side. See #4472.
+            //
+            // Use a strict plain-object guard (prototype-chain check) rather than just
+            // `typeof === 'object' && !Array.isArray()` — Date, URL, Map, Set, and
+            // class instances would otherwise pass through and end up as
+            // `structuredContent`, violating the protocol's JSON-object contract.
+            // The mirror discipline applies in `workflow-tools.ts adaptExecutorResult`.
+            const base = { content };
+            if (isPlainObject(result.details)) {
+                base.structuredContent = result.details;
+            }
+            if (result.isError === true)
+                base.isError = true;
+            return base;
         }
         catch (err) {
             // AbortError from a cancelled tool surfaces as a normal error — MCP

package/dist/resource-loader.d.ts

@@ -21,6 +21,6 @@ export declare function getNewerManagedResourceVersion(agentDir: string, current
  *
  * Inspectable: `ls ~/.gsd/agent/extensions/`
  */
-export declare function initResources(agentDir: string): void;
+export declare function initResources(agentDir: string, skillsDir?: string): void;
 export declare function hasStaleCompiledExtensionSiblings(extensionsDir: string, sourceDir?: string): boolean;
 export declare function buildResourceLoader(agentDir: string): DefaultResourceLoader;

package/dist/resource-loader.js

@@ -506,7 +506,7 @@ function pruneRemovedBundledExtensions(manifest, agentDir) {
  *
  * Inspectable: `ls ~/.gsd/agent/extensions/`
  */
-export function initResources(agentDir) {
+export function initResources(agentDir, skillsDir = join(homedir(), '.agents', 'skills')) {
     mkdirSync(agentDir, { recursive: true });
     const currentVersion = getBundledGsdVersion();
     const manifest = readManagedResourceManifest(agentDir);
@@ -538,13 +538,7 @@ export function initResources(agentDir) {
     // Sync bundled resources — overwrite so updates land on next launch.
     syncResourceDir(bundledExtensionsDir, join(agentDir, 'extensions'));
     syncResourceDir(join(resourcesDir, 'agents'), join(agentDir, 'agents'));
-    // Skills are no longer force-synced here. Users install skills via the
-    // skills.sh CLI (`npx skills add <repo>`) into ~/.agents/skills/ which
-    // is the industry-standard Agent Skills ecosystem directory.
-    //
-    // Migration from the legacy ~/.gsd/agent/skills/ directory is handled
-    // above the manifest check so it runs on every launch (including retries
-    // after partial copy failures).
+    syncResourceDir(join(resourcesDir, 'skills'), skillsDir);
     // Sync GSD-WORKFLOW.md to agentDir as a fallback for when GSD_WORKFLOW_PATH
     // env var is not set (e.g. fork/dev builds, alternative entry points).
     const workflowSrc = join(resourcesDir, 'GSD-WORKFLOW.md');

package/dist/resources/extensions/claude-code-cli/stream-adapter.js

@@ -637,6 +637,68 @@ function normalizeToolResultContent(content) {
     }
     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) {
+    const sibling = block.structuredContent ?? block.structured_content;
+    if (sibling && typeof sibling === "object" && !Array.isArray(sibling)) {
+        return sibling;
+    }
+    if (Array.isArray(block.content)) {
+        for (const item of block.content) {
+            if (!item || typeof item !== "object")
+                continue;
+            const sub = item;
+            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;
+            }
+        }
+    }
+    // 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) {
+    if (!item || typeof item !== "object")
+        return false;
+    const type = item.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) {
+    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) {
     const extracted = [];
@@ -657,8 +719,8 @@ export function extractToolResultsFromSdkUserMessage(message) {
         extracted.push({
             toolUseId,
             result: {
-                content: normalizeToolResultContent(block.content),
-                details: {},
+                content: normalizeToolResultContent(stripStructuredContentPseudoBlocks(block.content)),
+                details: extractStructuredDetailsFromBlock(block),
                 isError: block.is_error === true,
             },
         });
@@ -672,8 +734,8 @@ export function extractToolResultsFromSdkUserMessage(message) {
                 extracted.push({
                     toolUseId,
                     result: {
-                        content: normalizeToolResultContent(toolResult.content),
-                        details: {},
+                        content: normalizeToolResultContent(stripStructuredContentPseudoBlocks(toolResult.content)),
+                        details: extractStructuredDetailsFromBlock(toolResult),
                         isError: toolResult.is_error === true,
                     },
                 });

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

@@ -1094,7 +1094,7 @@ export async function runUnitPhase(ic, iterData, loopState, sidecarItem) {
         logWarning("engine", "Prompt reorder failed", { error: msg });
     }
     // Select and apply model (with tier escalation on retry — normal units only)
-    const modelResult = await deps.selectAndApplyModel(ctx, pi, unitType, unitId, s.basePath, prefs, s.verbose, s.autoModeStartModel, sidecarItem ? undefined : { isRetry, previousTier }, undefined, s.manualSessionModelOverride);
+    const modelResult = await deps.selectAndApplyModel(ctx, pi, unitType, unitId, s.basePath, prefs, s.verbose, s.autoModeStartModel, sidecarItem ? undefined : { isRetry, previousTier }, undefined, s.manualSessionModelOverride, s.autoModeStartThinkingLevel);
     s.currentUnitRouting =
         modelResult.routing;
     s.currentUnitModel =
@@ -1107,6 +1107,9 @@ export async function runUnitPhase(ic, iterData, loopState, sidecarItem) {
         if (match) {
             const ok = await pi.setModel(match, { persist: false });
             if (ok) {
+                if (s.autoModeStartThinkingLevel) {
+                    pi.setThinkingLevel(s.autoModeStartThinkingLevel);
+                }
                 s.currentUnitModel = match;
                 ctx.ui.notify(`Hook model override: ${match.provider}/${match.id}`, "info");
             }

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

@@ -65,6 +65,8 @@ export class AutoSession {
     currentDispatchedModelId = null;
     originalModelId = null;
     originalModelProvider = null;
+    autoModeStartThinkingLevel = null;
+    originalThinkingLevel = null;
     lastBudgetAlertLevel = 0;
     // ── Recovery ─────────────────────────────────────────────────────────────
     pendingCrashRecovery = null;
@@ -177,6 +179,8 @@ export class AutoSession {
         this.currentDispatchedModelId = null;
         this.originalModelId = null;
         this.originalModelProvider = null;
+        this.autoModeStartThinkingLevel = null;
+        this.originalThinkingLevel = null;
         this.lastBudgetAlertLevel = 0;
         // Recovery
         this.pendingCrashRecovery = null;

package/dist/resources/extensions/gsd/auto-model-selection.js

@@ -12,6 +12,12 @@ 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";
+function reapplyThinkingLevel(pi, level) {
+    if (!level)
+        return;
+    pi.setThinkingLevel(level);
+}
 export function resolvePreferredModelConfig(unitType, autoModeStartModel, isAutoMode = true) {
     const explicitConfig = resolveModelWithFallbacksForUnit(unitType);
     if (explicitConfig) {
@@ -57,7 +63,9 @@ export async function selectAndApplyModel(ctx, pi, unitType, unitId, basePath, p
  *  Dynamic routing only applies in auto-mode where cost optimization is expected. (#3962) */
 isAutoMode = true, 
 /** Explicit /gsd model pin captured at bootstrap for long-running auto loops. */
-sessionModelOverride) {
+sessionModelOverride, 
+/** Thinking level captured at auto-mode start and re-applied after model swaps. */
+autoModeStartThinkingLevel) {
     const uokFlags = resolveUokFlags(prefs);
     const effectiveSessionModelOverride = sessionModelOverride === undefined
         ? getSessionModelOverride(ctx.sessionManager.getSessionId())
@@ -260,6 +268,14 @@ sessionModelOverride) {
                 }
                 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);
@@ -271,6 +287,7 @@ sessionModelOverride) {
             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.
                 const activeToolNames = pi.getActiveTools();
@@ -325,19 +342,28 @@ sessionModelOverride) {
         // 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/dist/resources/extensions/gsd/auto-start.js

@@ -30,7 +30,7 @@ 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, enableDebug, isDebugEnabled, getDebugLogPath, } from "./debug-logger.js";
 import { logWarning, logError } from "./workflow-logger.js";
@@ -190,8 +190,8 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
     //
     // 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.
@@ -224,11 +224,14 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         }
     }
     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
         const customProjectId = process.env.GSD_PROJECT_ID;
@@ -244,7 +247,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // the parent git root). See #2393 and related issue.
         const hasLocalGit = existsSync(join(base, ".git"));
         if (!hasLocalGit || isInheritedRepo(base)) {
-            const mainBranch = loadEffectiveGSDPreferences()?.preferences?.git?.main_branch || "main";
+            const mainBranch = loadEffectiveGSDPreferences(base)?.preferences?.git?.main_branch || "main";
             nativeInit(base, mainBranch);
         }
         // Migrate legacy in-project .gsd/ to external state directory.
@@ -260,7 +263,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // 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)
@@ -286,7 +289,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             prepareWorkflowMcpForProject(ctx, base);
         }
         // Initialize GitServiceImpl
-        s.gitService = new GitServiceImpl(s.basePath, loadEffectiveGSDPreferences()?.preferences?.git ?? {});
+        s.gitService = new GitServiceImpl(s.basePath, loadEffectiveGSDPreferences(base)?.preferences?.git ?? {});
         // ── Debug mode ──
         if (!isDebugEnabled() && process.env.GSD_DEBUG === "1") {
             enableDebug(base);
@@ -319,7 +322,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // 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: ${msg}`, "info");
             }
@@ -337,7 +340,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         let state = await deriveState(base);
         // Stale worktree state recovery (#654)
         if (state.activeMilestone &&
-            shouldUseWorktreeIsolation() &&
+            shouldUseWorktreeIsolation(base) &&
             !detectWorktreeName(base)) {
             const wtPath = getAutoWorktreePath(base, state.activeMilestone.id);
             if (wtPath) {
@@ -352,7 +355,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         let hasSurvivorBranch = false;
         if (state.activeMilestone &&
             (state.phase === "pre-planning" || state.phase === "complete") &&
-            getIsolationMode() !== "none" &&
+            getIsolationMode(base) !== "none" &&
             !detectWorktreeName(base) &&
             !base.includes(`${pathSep}.gsd${pathSep}worktrees${pathSep}`)) {
             const milestoneBranch = `milestone/${state.activeMilestone.id}`;
@@ -506,13 +509,14 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         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);
@@ -520,7 +524,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // 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/")) {
@@ -548,7 +552,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             return symlinkRe.test(p);
         };
         if (s.currentMilestoneId &&
-            getIsolationMode() !== "none" &&
+            getIsolationMode(base) !== "none" &&
             !detectWorktreeName(base) &&
             !isUnderGsdWorktrees(base)) {
             buildResolver().enterMilestone(s.currentMilestoneId, {
@@ -593,8 +597,21 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // call returns "db_unavailable", triggering artifact-retry which
         // re-dispatches the same task — producing an infinite loop (#2419).
         if (existsSync(gsdDbPath) && !isDbAvailable()) {
-            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.", "error");
+            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: ${gsdDbPath}. ${phaseHint}${errorDetail}.${providerHint}`, "error");
             return releaseLockAndReturn();
         }
         // Initialize metrics
@@ -608,6 +625,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
                 id: startModelSnapshot.id,
             };
         }
+        s.autoModeStartThinkingLevel = startThinkingSnapshot ?? null;
         s.manualSessionModelOverride = manualSessionOverride ?? null;
         // Apply worker model override from parallel orchestrator (#worker-model).
         // GSD_WORKER_MODEL is injected by the coordinator when parallel.worker_model
@@ -628,7 +646,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             }
         }
         // Snapshot installed skills
-        if (resolveSkillDiscoveryMode() !== "off") {
+        if (resolveSkillDiscoveryMode(base) !== "off") {
             snapshotSkills();
         }
         ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
@@ -656,7 +674,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // 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

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

@@ -145,8 +145,8 @@ export function startAutoDetached(ctx, pi, base, verboseMode, options) {
     });
 }
 /** Returns true if the project is configured for `isolation:worktree` mode. */
-export function shouldUseWorktreeIsolation() {
-    const prefs = loadEffectiveGSDPreferences()?.preferences?.git;
+export function shouldUseWorktreeIsolation(basePath) {
+    const prefs = loadEffectiveGSDPreferences(basePath)?.preferences?.git;
     if (prefs?.isolation === "worktree")
         return true;
     // Default is false — worktree isolation requires explicit opt-in
@@ -215,7 +215,7 @@ export function getAutoDashboardData() {
     const rtkSavings = sessionId && s.basePath
         ? getRtkSessionSavings(s.basePath, sessionId)
         : null;
-    const rtkEnabled = loadEffectiveGSDPreferences()?.preferences.experimental?.rtk === true;
+    const rtkEnabled = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences.experimental?.rtk === true;
     // Pending capture count — lazy check, non-fatal
     let pendingCaptureCount = 0;
     try {
@@ -393,7 +393,7 @@ function clearUnitTimeout() {
 }
 /** Build snapshot metric opts. */
 function buildSnapshotOpts(_unitType, _unitId) {
-    const prefs = loadEffectiveGSDPreferences()?.preferences;
+    const prefs = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences;
     const uokFlags = resolveUokFlags(prefs);
     return {
         ...(s.autoStartTime > 0 ? { autoSessionKey: String(s.autoStartTime) } : {}),
@@ -427,7 +427,7 @@ function handleLostSessionLock(ctx, lockStatus) {
     restoreProjectRootEnv();
     restoreMilestoneLockEnv();
     deregisterSigtermHandler();
-    clearCmuxSidebar(loadEffectiveGSDPreferences()?.preferences);
+    clearCmuxSidebar(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences);
     const base = lockBase();
     const lockFilePath = base ? join(gsdRoot(base), "auto.lock") : "unknown";
     const recoverySuggestion = "\nTo recover, run: gsd doctor --fix";
@@ -498,7 +498,7 @@ function cleanupAfterLoopExit(ctx) {
 export async function stopAuto(ctx, pi, reason) {
     if (!s.active && !s.paused)
         return;
-    const loadedPreferences = loadEffectiveGSDPreferences()?.preferences;
+    const loadedPreferences = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences;
     const reasonSuffix = reason ? ` — ${reason}` : "";
     try {
         // ── Step 1: Timers and locks ──
@@ -695,13 +695,16 @@ export async function stopAuto(ctx, pi, reason) {
         catch (err) { /* non-fatal */
             logWarning("engine", `file unlink failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
         }
-        // ── Step 13: Restore original model (before reset clears IDs) ──
+        // ── Step 13: Restore original model + thinking (before reset clears IDs) ──
         try {
             if (pi && ctx && s.originalModelId && s.originalModelProvider) {
                 const original = ctx.modelRegistry.find(s.originalModelProvider, s.originalModelId);
                 if (original)
                     await pi.setModel(original);
             }
+            if (pi && s.originalThinkingLevel) {
+                pi.setThinkingLevel(s.originalThinkingLevel);
+            }
         }
         catch (e) {
             debugLog("stop-cleanup-model", { error: e instanceof Error ? e.message : String(e) });
@@ -1161,7 +1164,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         });
         // ── Auto-worktree / branch-mode: re-enter on resume ──
         if (s.currentMilestoneId &&
-            getIsolationMode() !== "none" &&
+            getIsolationMode(s.originalBasePath || s.basePath) !== "none" &&
             s.originalBasePath &&
             !isInAutoWorktree(s.basePath) &&
             !detectWorktreeName(s.basePath) &&
@@ -1194,7 +1197,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         await openProjectDbIfPresent(s.basePath);
         try {
             await rebuildState(s.basePath);
-            syncCmuxSidebar(loadEffectiveGSDPreferences()?.preferences, await deriveState(s.basePath));
+            syncCmuxSidebar(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, await deriveState(s.basePath));
         }
         catch (e) {
             debugLog("resume-rebuild-state-failed", {
@@ -1224,7 +1227,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         }
         updateSessionLock(lockBase(), "resuming", s.currentMilestoneId ?? "unknown");
         writeLock(lockBase(), "resuming", s.currentMilestoneId ?? "unknown");
-        logCmuxEvent(loadEffectiveGSDPreferences()?.preferences, s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", "progress");
+        logCmuxEvent(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", "progress");
         captureProjectRootEnv(s.originalBasePath || s.basePath);
         startAutoCommandPolling(s.basePath);
         await runAutoLoopWithUok({
@@ -1250,13 +1253,13 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         return;
     captureProjectRootEnv(s.originalBasePath || s.basePath);
     try {
-        syncCmuxSidebar(loadEffectiveGSDPreferences()?.preferences, await deriveState(s.basePath));
+        syncCmuxSidebar(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, await deriveState(s.basePath));
     }
     catch (err) {
         // Best-effort only — sidebar sync must never block auto-mode startup
         logWarning("engine", `cmux sync failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
     }
-    logCmuxEvent(loadEffectiveGSDPreferences()?.preferences, requestedStepMode ? "Step-mode started." : "Auto-mode started.", "progress");
+    logCmuxEvent(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, requestedStepMode ? "Step-mode started." : "Auto-mode started.", "progress");
     startAutoCommandPolling(s.basePath);
     // Dispatch the first unit
     await runAutoLoopWithUok({