diff --git a/packages/pi-coding-agent/src/modes/interactive/components/extension-input.ts b/packages/pi-coding-agent/src/modes/interactive/components/extension-input.ts
index 4c0e816bd..06d7ee933 100644
--- a/packages/pi-coding-agent/src/modes/interactive/components/extension-input.ts
+++ b/packages/pi-coding-agent/src/modes/interactive/components/extension-input.ts
@@ -33,7 +33,7 @@ export class ExtensionInputComponent extends Container implements Focusable {
 
 	constructor(
 		title: string,
-		_placeholder: string | undefined,
+		placeholder: string | undefined,
 		onSubmit: (value: string) => void,
 		onCancel: () => void,
 		opts?: ExtensionInputOptions,
@@ -61,6 +61,9 @@ export class ExtensionInputComponent extends Container implements Focusable {
 		}
 
 		this.input = new Input();
+		if (placeholder) {
+			this.input.placeholder = placeholder;
+		}
 		this.addChild(this.input);
 		this.addChild(new Spacer(1));
 		this.addChild(new Text(`${keyHint("selectConfirm", "submit")}  ${keyHint("selectCancel", "cancel")}`, 1, 0));
diff --git a/packages/pi-coding-agent/src/modes/interactive/interactive-mode.ts b/packages/pi-coding-agent/src/modes/interactive/interactive-mode.ts
index 4d098f59c..3f7a37848 100644
--- a/packages/pi-coding-agent/src/modes/interactive/interactive-mode.ts
+++ b/packages/pi-coding-agent/src/modes/interactive/interactive-mode.ts
@@ -998,9 +998,20 @@ export class InteractiveMode {
 		if (showDiagnostics) {
 			const skillDiagnostics = skillsResult.diagnostics;
 			if (skillDiagnostics.length > 0) {
-				const warningLines = this.formatDiagnostics(skillDiagnostics, metadata);
-				this.chatContainer.addChild(new Text(`${theme.fg("warning", "[Skill conflicts]")}\n${warningLines}`, 0, 0));
-				this.chatContainer.addChild(new Spacer(1));
+				const collisionDiags = skillDiagnostics.filter(d => d.type === "collision");
+				const issueDiags = skillDiagnostics.filter(d => d.type !== "collision");
+
+				if (collisionDiags.length > 0) {
+					const collisionLines = this.formatDiagnostics(collisionDiags, metadata);
+					this.chatContainer.addChild(new Text(`${theme.fg("warning", "[Skill conflicts]")}\n${collisionLines}`, 0, 0));
+					this.chatContainer.addChild(new Spacer(1));
+				}
+
+				if (issueDiags.length > 0) {
+					const issueLines = this.formatDiagnostics(issueDiags, metadata);
+					this.chatContainer.addChild(new Text(`${theme.fg("warning", "[Skill issues]")}\n${issueLines}`, 0, 0));
+					this.chatContainer.addChild(new Spacer(1));
+				}
 			}
 
 			const promptDiagnostics = promptsResult.diagnostics;
diff --git a/packages/pi-tui/src/components/input.ts b/packages/pi-tui/src/components/input.ts
index e5c3b4f7f..13714b138 100644
--- a/packages/pi-tui/src/components/input.ts
+++ b/packages/pi-tui/src/components/input.ts
@@ -20,6 +20,7 @@ export class Input implements Component, Focusable {
 	private cursor: number = 0; // Cursor position in the value
 	public onSubmit?: (value: string) => void;
 	public onEscape?: () => void;
+	public placeholder: string = "";
 
 	/** Focusable interface - set by TUI when focus changes */
 	focused: boolean = false;
@@ -440,6 +441,16 @@ export class Input implements Component, Focusable {
 			return [prompt];
 		}
 
+		// Show placeholder when value is empty
+		if (this.value === "" && this.placeholder) {
+			const placeholderText = this.placeholder.slice(0, availableWidth - 1);
+			const marker = this.focused ? CURSOR_MARKER : "";
+			const cursorChar = "\x1b[7m \x1b[27m"; // inverse space for cursor
+			const dimPlaceholder = `\x1b[2m${placeholderText}\x1b[22m`; // dim text
+			const padding = " ".repeat(Math.max(0, availableWidth - visibleWidth(placeholderText) - 1));
+			return [prompt + marker + cursorChar + dimPlaceholder + padding];
+		}
+
 		let visibleText = "";
 		let cursorDisplay = this.cursor;
 
diff --git a/src/resources/extensions/gsd/commands.ts b/src/resources/extensions/gsd/commands.ts
index 1ebb86f09..c42ea113e 100644
--- a/src/resources/extensions/gsd/commands.ts
+++ b/src/resources/extensions/gsd/commands.ts
@@ -215,20 +215,16 @@ export async function fireStatusViaCommand(
 async function handlePrefs(args: string, ctx: ExtensionCommandContext): Promise<void> {
   const trimmed = args.trim();
 
-  if (trimmed === "" || trimmed === "global") {
+  if (trimmed === "" || trimmed === "global" || trimmed === "wizard" || trimmed === "setup"
+    || trimmed === "wizard global" || trimmed === "setup global") {
     await ensurePreferencesFile(getGlobalGSDPreferencesPath(), ctx, "global");
+    await handlePrefsWizard(ctx, "global");
     return;
   }
 
-  if (trimmed === "project") {
+  if (trimmed === "project" || trimmed === "wizard project" || trimmed === "setup project") {
     await ensurePreferencesFile(getProjectGSDPreferencesPath(), ctx, "project");
-    return;
-  }
-
-  if (trimmed === "wizard" || trimmed === "setup" || trimmed === "wizard global" || trimmed === "setup global"
-    || trimmed === "wizard project" || trimmed === "setup project") {
-    const scope = trimmed.includes("project") ? "project" : "global";
-    await handlePrefsWizard(ctx, scope);
+    await handlePrefsWizard(ctx, "project");
     return;
   }
 
@@ -319,22 +315,41 @@ async function handlePrefsWizard(
   const modelPhases = ["research", "planning", "execution", "completion"] as const;
   const models: Record<string, string> = (prefs.models as Record<string, string>) ?? {};
 
-  for (const phase of modelPhases) {
-    const current = models[phase] ?? "";
-    const input = await ctx.ui.input(
-      `Model for ${phase} phase${current ? ` (current: ${current})` : ""}:`,
-      current || "e.g. claude-sonnet-4-20250514",
-    );
-    if (input !== null && input !== undefined) {
-      const val = input.trim();
-      if (val) {
-        models[phase] = val;
-      } else if (current) {
-        // User cleared it — remove
-        delete models[phase];
+  const availableModels = ctx.modelRegistry.getAvailable();
+  if (availableModels.length > 0) {
+    const modelOptions = availableModels.map(m => `${m.id} · ${m.provider}`);
+    modelOptions.push("(keep current)", "(clear)");
+
+    for (const phase of modelPhases) {
+      const current = models[phase] ?? "";
+      const title = `Model for ${phase} phase${current ? ` (current: ${current})` : ""}:`;
+      const choice = await ctx.ui.select(title, modelOptions);
+
+      if (choice && choice !== "(keep current)") {
+        if (choice === "(clear)") {
+          delete models[phase];
+        } else {
+          models[phase] = choice.split(" · ")[0];
+        }
+      }
+    }
+  } else {
+    // No authenticated models available — fall back to text input
+    for (const phase of modelPhases) {
+      const current = models[phase] ?? "";
+      const input = await ctx.ui.input(
+        `Model for ${phase} phase${current ? ` (current: ${current})` : ""}:`,
+        current || "e.g. claude-sonnet-4-20250514",
+      );
+      if (input !== null && input !== undefined) {
+        const val = input.trim();
+        if (val) {
+          models[phase] = val;
+        } else if (current) {
+          delete models[phase];
+        }
       }
     }
-    // null/undefined = Escape/skip — keep existing value
   }
   if (Object.keys(models).length > 0) {
     prefs.models = models;
@@ -452,8 +467,7 @@ function serializePreferencesToFrontmatter(prefs: Record<string, unknown>): stri
 
     if (Array.isArray(value)) {
       if (value.length === 0) {
-        lines.push(`${prefix}${key}: []`);
-        return;
+        return; // Omit empty arrays — avoids parse/serialize cycle bug with "[]" strings
       }
       lines.push(`${prefix}${key}:`);
       for (const item of value) {
@@ -484,8 +498,7 @@ function serializePreferencesToFrontmatter(prefs: Record<string, unknown>): stri
     if (typeof value === "object") {
       const entries = Object.entries(value as Record<string, unknown>);
       if (entries.length === 0) {
-        lines.push(`${prefix}${key}: {}`);
-        return;
+        return; // Omit empty objects — avoids parse/serialize cycle bug with "{}" strings
       }
       lines.push(`${prefix}${key}:`);
       for (const [k, v] of entries) {
@@ -538,7 +551,4 @@ async function ensurePreferencesFile(
     ctx.ui.notify(`Using existing ${scope} GSD skill preferences at ${path}`, "info");
   }
 
-  await ctx.waitForIdle();
-  await ctx.reload();
-  ctx.ui.notify(`Edit ${path} to update ${scope} GSD skill preferences.`, "info");
 }
diff --git a/src/resources/extensions/gsd/preferences.ts b/src/resources/extensions/gsd/preferences.ts
index f2f7bef66..2f06c7154 100644
--- a/src/resources/extensions/gsd/preferences.ts
+++ b/src/resources/extensions/gsd/preferences.ts
@@ -482,16 +482,20 @@ function parseFrontmatterBlock(frontmatter: string): GSDPreferences {
   return root as GSDPreferences;
 }
 
-function parseScalar(value: string): string | number | boolean {
+function parseScalar(value: string): unknown {
   if (value === "true") return true;
   if (value === "false") return false;
+  // Recognize empty array/object literals (with or without surrounding quotes)
+  const unquoted = value.replace(/^['\"]|['\"]$/g, "");
+  if (unquoted === "[]") return [];
+  if (unquoted === "{}") return {};
   if (/^-?\d+$/.test(value)) {
     const n = Number(value);
     // Keep large integers (e.g. Discord channel IDs) as strings to avoid precision loss
     if (Number.isSafeInteger(n)) return n;
     return value;
   }
-  return value.replace(/^['\"]|['\"]$/g, "");
+  return unquoted;
 }
 
 /**