diff --git a/patches/@mariozechner+pi-coding-agent+0.57.1.patch b/patches/@mariozechner+pi-coding-agent+0.57.1.patch
index 0216c88d9..0b2a0a8c8 100644
--- a/patches/@mariozechner+pi-coding-agent+0.57.1.patch
+++ b/patches/@mariozechner+pi-coding-agent+0.57.1.patch
@@ -1,3 +1,63 @@
+diff --git a/node_modules/@mariozechner/pi-coding-agent/dist/core/agent-session.js b/node_modules/@mariozechner/pi-coding-agent/dist/core/agent-session.js
+index 90622c2..cff094b 100644
+--- a/node_modules/@mariozechner/pi-coding-agent/dist/core/agent-session.js
++++ b/node_modules/@mariozechner/pi-coding-agent/dist/core/agent-session.js
+@@ -1007,7 +1007,7 @@ export class AgentSession {
+      * Validates API key, saves to session and settings.
+      * @throws Error if no API key available for the model
+      */
+-    async setModel(model) {
++    async setModel(model, options) {
+         const apiKey = await this._modelRegistry.getApiKey(model);
+         if (!apiKey) {
+             throw new Error(`No API key for ${model.provider}/${model.id}`);
+@@ -1016,7 +1016,9 @@ export class AgentSession {
+         const thinkingLevel = this._getThinkingLevelForModelSwitch();
+         this.agent.setModel(model);
+         this.sessionManager.appendModelChange(model.provider, model.id);
+-        this.settingsManager.setDefaultModelAndProvider(model.provider, model.id);
++        if (options?.persist !== false) {
++            this.settingsManager.setDefaultModelAndProvider(model.provider, model.id);
++        }
+         // Re-clamp thinking level for new model's capabilities
+         this.setThinkingLevel(thinkingLevel);
+         await this._emitModelSelect(model, previousModel, "set");
+@@ -1067,7 +1069,9 @@ export class AgentSession {
+         // Apply model
+         this.agent.setModel(next.model);
+         this.sessionManager.appendModelChange(next.model.provider, next.model.id);
+-        this.settingsManager.setDefaultModelAndProvider(next.model.provider, next.model.id);
++        if (options?.persist !== false) {
++            this.settingsManager.setDefaultModelAndProvider(next.model.provider, next.model.id);
++        }
+         // Apply thinking level.
+         // - Explicit scoped model thinking level overrides current session level
+         // - Undefined scoped model thinking level inherits the current session preference
+@@ -1094,7 +1098,9 @@ export class AgentSession {
+         const thinkingLevel = this._getThinkingLevelForModelSwitch();
+         this.agent.setModel(nextModel);
+         this.sessionManager.appendModelChange(nextModel.provider, nextModel.id);
+-        this.settingsManager.setDefaultModelAndProvider(nextModel.provider, nextModel.id);
++        if (options?.persist !== false) {
++            this.settingsManager.setDefaultModelAndProvider(nextModel.provider, nextModel.id);
++        }
+         // Re-clamp thinking level for new model's capabilities
+         this.setThinkingLevel(thinkingLevel);
+         await this._emitModelSelect(nextModel, currentModel, "cycle");
+@@ -1659,11 +1665,11 @@ export class AgentSession {
+             setActiveTools: (toolNames) => this.setActiveToolsByName(toolNames),
+             refreshTools: () => this._refreshToolRegistry(),
+             getCommands,
+-            setModel: async (model) => {
++            setModel: async (model, options) => {
+                 const key = await this.modelRegistry.getApiKey(model);
+                 if (!key)
+                     return false;
+-                await this.setModel(model);
++                await this.setModel(model, options);
+                 return true;
+             },
+             getThinkingLevel: () => this.thinkingLevel,
 diff --git a/node_modules/@mariozechner/pi-coding-agent/dist/core/tools/bash.js b/node_modules/@mariozechner/pi-coding-agent/dist/core/tools/bash.js
 index 27fe820..68f277f 100644
 --- a/node_modules/@mariozechner/pi-coding-agent/dist/core/tools/bash.js
diff --git a/src/resources/extensions/gsd/auto.ts b/src/resources/extensions/gsd/auto.ts
index 910cdc931..b628d16ec 100644
--- a/src/resources/extensions/gsd/auto.ts
+++ b/src/resources/extensions/gsd/auto.ts
@@ -247,6 +247,14 @@ export async function startAuto(
     if (!getLedger()) initMetrics(base);
     ctx.ui.setStatus("gsd-auto", stepMode ? "next" : "auto");
     ctx.ui.notify(stepMode ? "Step-mode resumed." : "Auto-mode resumed.", "info");
+    // Rebuild disk state before resuming — user interaction during pause may have changed files
+    try { await rebuildState(base); } catch { /* non-fatal */ }
+    try {
+      const report = await runGSDDoctor(base, { fix: true });
+      if (report.fixesApplied.length > 0) {
+        ctx.ui.notify(`Resume: applied ${report.fixesApplied.length} fix(es) to state.`, "info");
+      }
+    } catch { /* non-fatal */ }
     await dispatchNextUnit(ctx, pi);
     return;
   }
@@ -758,7 +766,12 @@ async function dispatchNextUnit(
   ctx: ExtensionContext,
   pi: ExtensionAPI,
 ): Promise<void> {
-  if (!active || !cmdCtx) return;
+  if (!active || !cmdCtx) {
+    if (active && !cmdCtx) {
+      ctx.ui.notify("Auto-mode dispatch failed: no command context. Run /gsd auto to restart.", "error");
+    }
+    return;
+  }
 
   let state = await deriveState(basePath);
   let mid = state.activeMilestone?.id;
@@ -1086,7 +1099,7 @@ async function dispatchNextUnit(
     const allModels = ctx.modelRegistry.getAll();
     const model = allModels.find(m => m.id === preferredModelId);
     if (model) {
-      const ok = await pi.setModel(model);
+      const ok = await pi.setModel(model, { persist: false });
       if (ok) {
         ctx.ui.notify(`Model: ${preferredModelId}`, "info");
       }
@@ -1186,7 +1199,8 @@ async function dispatchNextUnit(
     await pauseAuto(ctx, pi);
   }, hardTimeoutMs);
 
-  // Inject prompt
+  // Inject prompt — verify auto-mode still active (guards against race with timeout/pause)
+  if (!active) return;
   pi.sendMessage(
     { customType: "gsd-auto", content: finalPrompt, display: verbose },
     { triggerTurn: true },