diff --git a/AGENTS.md b/AGENTS.md
index cc8307e..3a61264 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -81,4 +81,5 @@ The domain model (Host, Module, Skeleton, Auto-loader, Enable convention, overla
 - Flake-managed Pi extension, prompt, and skill directories may still be written directly for throwaway development or local experiments.
   The risk is that a later Home Manager activation can overwrite or hide those unmanaged files, so finished work must be promoted into the dotfiles module before it counts as deployed.
 - Pi's tool discovery checks `~/.pi/agent/bin` before `PATH`, and downloaded generic Linux binaries there can be unusable on NixOS with the stub-ld error.
-  A copied or patched Pi launcher that only prepends Nix `fd`/`rg` to `PATH` may still break `@` autocomplete unless the local tool path is removed or Pi validates the local binary before using it.
+  This flake patches Pi to validate local tool binaries before selecting them, so it falls back to usable `fd`/`rg` from `PATH` instead.
+  Stale unpatched launchers are the remaining failure mode for broken `@` autocomplete.
diff --git a/modules/agents/pi/patches/pi-flex-spacer.patch b/modules/agents/pi/patches/pi-flex-spacer.patch
new file mode 100644
index 0000000..1c2d733
--- /dev/null
+++ b/modules/agents/pi/patches/pi-flex-spacer.patch
@@ -0,0 +1,169 @@
+diff --git a/packages/tui/src/tui.ts b/packages/tui/src/tui.ts
+--- a/packages/tui/src/tui.ts	2026-08-02 00:16:00.000000000 -0400
++++ b/packages/tui/src/tui.ts	2026-08-02 00:16:00.000000000 -0400
+@@ -310,7 +310,7 @@ export class TUI extends Container {
+ 	private cursorRow = 0; // Logical cursor row (end of rendered content)
+ 	private hardwareCursorRow = 0; // Actual terminal cursor row (may differ due to IME positioning)
+ 	private showHardwareCursor = process.env.PI_HARDWARE_CURSOR === "1";
+-	private clearOnShrink = process.env.PI_CLEAR_ON_SHRINK === "1"; // Clear empty rows when content shrinks (default: off)
++	private clearOnShrink = process.env.PI_CLEAR_ON_SHRINK !== "0"; // Clear empty rows when content shrinks (default: on)
+ 	private maxLinesRendered = 0; // Track terminal's working area (max lines ever rendered)
+ 	private previousViewportTop = 0; // Track previous viewport top for resize-aware cursor moves
+ 	private fullRedrawCount = 0;
+
+diff --git a/packages/coding-agent/src/core/settings-manager.ts b/packages/coding-agent/src/core/settings-manager.ts
+--- a/packages/coding-agent/src/core/settings-manager.ts	2026-08-02 00:34:00.000000000 -0400
++++ b/packages/coding-agent/src/core/settings-manager.ts	2026-08-02 00:34:00.000000000 -0400
+@@ -1093,11 +1093,11 @@ export class SettingsManager {
+ 	}
+ 
+ 	getClearOnShrink(): boolean {
+-		// Settings takes precedence, then env var, then default false
++		// Settings takes precedence, then env var, then default true
+ 		if (this.settings.terminal?.clearOnShrink !== undefined) {
+ 			return this.settings.terminal.clearOnShrink;
+ 		}
+-		return process.env.PI_CLEAR_ON_SHRINK === "1";
++		return process.env.PI_CLEAR_ON_SHRINK !== "0";
+ 	}
+ 
+ 	setClearOnShrink(enabled: boolean): void {
+
+diff --git a/packages/coding-agent/src/modes/interactive/interactive-mode.ts b/packages/coding-agent/src/modes/interactive/interactive-mode.ts
+--- a/packages/coding-agent/src/modes/interactive/interactive-mode.ts	2026-08-01 18:41:36.963495957 -0400
++++ b/packages/coding-agent/src/modes/interactive/interactive-mode.ts	2026-08-01 18:43:04.876341236 -0400
+@@ -210,6 +210,45 @@
+ 	return code !== undefined && DEAD_TERMINAL_ERROR_CODES.has(code);
+ }
+ 
++class FlexSpacerBottomLayout implements Component {
++	private readonly ui: TUI;
++	private readonly flowChildren: Component[];
++	private readonly pinnedChildren: Component[];
++
++	constructor(ui: TUI, flowChildren: Component[], pinnedChildren: Component[]) {
++		this.ui = ui;
++		this.flowChildren = flowChildren;
++		this.pinnedChildren = pinnedChildren;
++	}
++
++	invalidate(): void {
++		for (const child of [...this.flowChildren, ...this.pinnedChildren]) {
++			child.invalidate();
++		}
++	}
++
++	private renderGroup(children: Component[], width: number): string[] {
++		const lines: string[] = [];
++		for (const child of children) {
++			lines.push(...child.render(width));
++		}
++		return lines;
++	}
++
++	render(width: number): string[] {
++		const flowLines = this.renderGroup(this.flowChildren, width);
++		const pinnedLines = this.renderGroup(this.pinnedChildren, width);
++		const terminalRows = this.ui.terminal.rows;
++		const spacerRows = Math.max(0, terminalRows - flowLines.length - pinnedLines.length);
++
++		return [
++			...flowLines,
++			...Array.from({ length: spacerRows }, () => ""),
++			...pinnedLines,
++		];
++	}
++}
++
+ const ANTHROPIC_SUBSCRIPTION_AUTH_WARNING =
+ 	"Anthropic subscription auth is active. Third-party harness usage draws from extra usage and is billed per token, not your Claude plan limits. Manage extra usage at https://claude.ai/settings/usage. Disable this warning in /settings.";
+ 
+@@ -335,6 +374,7 @@
+ 	private fdPath: string | undefined;
+ 	private editorContainer: Container;
+ 	private footer: FooterComponent;
++	private footerContainer: Container;
+ 	private footerDataProvider: FooterDataProvider;
+ 	// Stored so the same manager can be injected into custom editors, selectors, and extension UI.
+ 	private keybindings: KeybindingsManager;
+@@ -477,7 +517,9 @@
+ 		this.editorContainer = new Container();
+ 		this.editorContainer.addChild(this.editor as Component);
+ 		this.footerDataProvider = new FooterDataProvider(this.sessionManager.getCwd());
++		this.footerContainer = new Container();
+ 		this.footer = new FooterComponent(this.session, this.footerDataProvider);
++		this.footerContainer.addChild(this.footer);
+ 		this.footer.setAutoCompactEnabled(this.session.autoCompactionEnabled);
+ 
+ 		// Load hide thinking block setting
+@@ -704,19 +746,25 @@
+ 			console.log(theme.fg("dim", `Model scope: ${modelList}${cycleHint}`));
+ 		}
+ 
+-		// Add header container as first child. Populate it after applying theme settings.
+-		// Keep loaded resources before chat so restored session messages never precede them.
+-		this.ui.addChild(this.headerContainer);
+-		this.ui.addChild(this.loadedResourcesContainer);
+-
+-		this.ui.addChild(this.chatContainer);
+-		this.ui.addChild(this.pendingMessagesContainer);
+-		this.ui.addChild(this.statusContainer);
+ 		this.renderWidgets(); // Initialize with default spacer
+-		this.ui.addChild(this.widgetContainerAbove);
+-		this.ui.addChild(this.editorContainer);
+-		this.ui.addChild(this.widgetContainerBelow);
+-		this.ui.addChild(this.footer);
++		this.ui.addChild(
++			new FlexSpacerBottomLayout(
++				this.ui,
++				[
++					this.headerContainer,
++					this.loadedResourcesContainer,
++					this.chatContainer,
++				],
++				[
++					this.pendingMessagesContainer,
++					this.statusContainer,
++					this.widgetContainerAbove,
++					this.editorContainer,
++					this.widgetContainerBelow,
++					this.footerContainer,
++				],
++			),
++		);
+ 		this.ui.setFocus(this.editor);
+ 
+ 		this.setupKeyHandlers();
+@@ -2033,25 +2081,25 @@
+ 			| ((tui: TUI, thm: Theme, footerData: ReadonlyFooterDataProvider) => Component & { dispose?(): void })
+ 			| undefined,
+ 	): void {
+-		// Dispose existing custom footer
++		// Dispose existing custom footer
+ 		if (this.customFooter?.dispose) {
+ 			this.customFooter.dispose();
+ 		}
+ 
+-		// Remove current footer from UI
++		// Remove current footer from its pinned layout slot.
+ 		if (this.customFooter) {
+-			this.ui.removeChild(this.customFooter);
++			this.footerContainer.removeChild(this.customFooter);
+ 		} else {
+-			this.ui.removeChild(this.footer);
++			this.footerContainer.removeChild(this.footer);
+ 		}
+ 
+ 		if (factory) {
+ 			// Create and add custom footer, passing the data provider
+ 			this.customFooter = factory(this.ui, theme, this.footerDataProvider);
+-			this.ui.addChild(this.customFooter);
++			this.footerContainer.addChild(this.customFooter);
+ 		} else {
+ 			// Restore built-in footer
+ 			this.customFooter = undefined;
+-			this.ui.addChild(this.footer);
++			this.footerContainer.addChild(this.footer);
+ 		}
+ 
+ 		this.ui.requestRender();
diff --git a/modules/agents/pi/patches/pi-tool-lookup-validation.patch b/modules/agents/pi/patches/pi-tool-lookup-validation.patch
new file mode 100644
index 0000000..9364a7e
--- /dev/null
+++ b/modules/agents/pi/patches/pi-tool-lookup-validation.patch
@@ -0,0 +1,22 @@
+diff --git a/packages/coding-agent/src/utils/tools-manager.ts b/packages/coding-agent/src/utils/tools-manager.ts
+--- a/packages/coding-agent/src/utils/tools-manager.ts	2026-08-01 18:41:36.970496010 -0400
++++ b/packages/coding-agent/src/utils/tools-manager.ts	2026-08-01 18:41:37.028186009 -0400
+@@ -74,8 +74,7 @@
+ function commandExists(cmd: string): boolean {
+ 	try {
+ 		const result = spawnSync(cmd, ["--version"], { stdio: "pipe" });
+-		// Check for ENOENT error (command not found)
+-		return result.error === undefined || result.error === null;
++		return (result.error === undefined || result.error === null) && result.status === 0;
+ 	} catch {
+ 		return false;
+ 	}
+@@ -88,7 +87,7 @@
+ 
+ 	// Check our tools directory first
+ 	const localPath = join(TOOLS_DIR, config.binaryName + (platform() === "win32" ? ".exe" : ""));
+-	if (existsSync(localPath)) {
++	if (existsSync(localPath) && commandExists(localPath)) {
+ 		return localPath;
+ 	}
+ 
diff --git a/modules/agents/pi/pi.nix b/modules/agents/pi/pi.nix
index a880d0c..293d74f 100644
--- a/modules/agents/pi/pi.nix
+++ b/modules/agents/pi/pi.nix
@@ -11,6 +11,12 @@ let
   cfg = config.modules.agents.pi;
   user = config.user.name;
   piDir = "${config.users.users.${user}.home}/.pi/agent";
+  patchedPi = pkgs.pi-coding-agent.overrideAttrs (old: {
+    patches = (old.patches or [ ]) ++ [
+      ./patches/pi-flex-spacer.patch
+      ./patches/pi-tool-lookup-validation.patch
+    ];
+  });
   herdrPiIntegration = pkgs.stdenvNoCC.mkDerivation {
     name = "herdr-pi-integration";
     nativeBuildInputs = [ pkgs.herdr ];
@@ -40,6 +46,7 @@ in
     home-manager.users.${user} = {
       programs.pi-coding-agent = {
         enable = true;
+        package = patchedPi;
 
         settings = {
           defaultProvider = "openai-codex";
diff --git a/modules/agents/pi/tests/autocomplete-bottom-alignment.test.sh b/modules/agents/pi/tests/autocomplete-bottom-alignment.test.sh
new file mode 100755
index 0000000..734c5cf
--- /dev/null
+++ b/modules/agents/pi/tests/autocomplete-bottom-alignment.test.sh
@@ -0,0 +1,240 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+repo_root=$(git rev-parse --show-toplevel)
+cd "$repo_root"
+
+pi_package=$(nix build --no-link --print-out-paths .#nixosConfigurations.neogaia.config.home-manager.users.alexion.programs.pi-coding-agent.package)
+tmpdir=$(mktemp -d)
+trap 'rm -rf "$tmpdir"' EXIT
+
+cat > "$tmpdir/autocomplete-bottom-alignment.mjs" <<'JS'
+import assert from "node:assert/strict";
+import { pathToFileURL } from "node:url";
+
+const piPackage = process.env.PI_PACKAGE;
+const tuiModuleUrl = pathToFileURL(
+	`${piPackage}/lib/node_modules/pi-monorepo/node_modules/@earendil-works/pi-tui/dist/index.js`,
+).href;
+const settingsModuleUrl = pathToFileURL(
+	`${piPackage}/lib/node_modules/pi-monorepo/dist/core/settings-manager.js`,
+).href;
+const { Editor, TUI } = await import(tuiModuleUrl);
+const { SettingsManager } = await import(settingsModuleUrl);
+
+if (process.env.PI_CLEAR_ON_SHRINK !== "0") {
+	assert.equal(SettingsManager.inMemory().getClearOnShrink(), true, "interactive sessions should enable shrink clearing by default");
+}
+
+class VirtualTerminal {
+	constructor(columns, rows) {
+		this._columns = columns;
+		this._rows = rows;
+		this.cursorRow = 0;
+		this.cursorCol = 0;
+		this.screen = Array.from({ length: rows }, () => Array(columns).fill(" "));
+	}
+
+	start(onInput, onResize) {
+		this.inputHandler = onInput;
+		this.resizeHandler = onResize;
+	}
+
+	async drainInput() {}
+	stop() {}
+	write(data) { this.applyOutput(data); }
+	get columns() { return this._columns; }
+	get rows() { return this._rows; }
+	get kittyProtocolActive() { return false; }
+	moveBy(lines) { this.moveCursor(lines, 0); }
+	hideCursor() {}
+	showCursor() {}
+	clearLine() { this.clearLineFromCursor(); }
+	setTitle() {}
+	setProgress() {}
+	sendInput(data) { this.inputHandler?.(data); }
+
+	async waitForRender() {
+		await new Promise((resolve) => process.nextTick(resolve));
+		await new Promise((resolve) => setTimeout(resolve, 30));
+	}
+
+	getViewport() {
+		return this.screen.map((line) => line.join(""));
+	}
+
+	applyOutput(data) {
+		for (let i = 0; i < data.length; i += 1) {
+			const char = data[i];
+			if (char === "\x1b") {
+				i = this.consumeEscape(data, i);
+			} else if (char === "\r") {
+				this.cursorCol = 0;
+			} else if (char === "\n") {
+				this.newline();
+			} else if (char >= " ") {
+				this.putChar(char);
+			}
+		}
+	}
+
+	consumeEscape(data, index) {
+		const next = data[index + 1];
+		if (next === "[") {
+			let end = index + 2;
+			while (end < data.length && !/[A-Za-z]/.test(data[end])) end += 1;
+			if (end < data.length) this.applyCsi(data.slice(index + 2, end), data[end]);
+			return end;
+		}
+		if (next === "]" || next === "_") {
+			const end = data.indexOf("\x07", index + 2);
+			return end === -1 ? data.length - 1 : end;
+		}
+		return index + 1;
+	}
+
+	applyCsi(params, command) {
+		const cleanParams = params.replace(/^\?/, "");
+		const values = cleanParams.length === 0 ? [] : cleanParams.split(";").map((value) => Number(value) || 0);
+		const first = values[0] || 1;
+		if (command === "A") this.moveCursor(-first, 0);
+		else if (command === "B") this.moveCursor(first, 0);
+		else if (command === "G") this.cursorCol = this.clamp(first - 1, 0, this.columns - 1);
+		else if (command === "H") {
+			this.cursorRow = this.clamp((values[0] || 1) - 1, 0, this.rows - 1);
+			this.cursorCol = this.clamp((values[1] || 1) - 1, 0, this.columns - 1);
+		} else if (command === "K") {
+			if (values[0] === 2) this.screen[this.cursorRow].fill(" ");
+			else this.clearLineFromCursor();
+		} else if (command === "J") {
+			if (values[0] === 2 || values[0] === 3) this.clearScreen();
+			else this.clearFromCursor();
+		}
+	}
+
+	putChar(char) {
+		this.screen[this.cursorRow][this.cursorCol] = char;
+		if (this.cursorCol < this.columns - 1) this.cursorCol += 1;
+	}
+
+	newline() {
+		if (this.cursorRow === this.rows - 1) {
+			this.screen.shift();
+			this.screen.push(Array(this.columns).fill(" "));
+		} else {
+			this.cursorRow += 1;
+		}
+	}
+
+	moveCursor(rowDelta, colDelta) {
+		this.cursorRow = this.clamp(this.cursorRow + rowDelta, 0, this.rows - 1);
+		this.cursorCol = this.clamp(this.cursorCol + colDelta, 0, this.columns - 1);
+	}
+
+	clearLineFromCursor() {
+		this.screen[this.cursorRow].fill(" ", this.cursorCol);
+	}
+
+	clearFromCursor() {
+		this.clearLineFromCursor();
+		for (let row = this.cursorRow + 1; row < this.rows; row += 1) {
+			this.screen[row].fill(" ");
+		}
+	}
+
+	clearScreen() {
+		for (const line of this.screen) line.fill(" ");
+		this.cursorRow = 0;
+		this.cursorCol = 0;
+	}
+
+	clamp(value, min, max) {
+		return Math.max(min, Math.min(max, value));
+	}
+}
+
+class Lines {
+	constructor(lines) { this.lines = lines; }
+	render() { return this.lines; }
+	invalidate() {}
+}
+
+class BottomLayout {
+	constructor(tui, flowChildren, pinnedChildren) {
+		this.tui = tui;
+		this.flowChildren = flowChildren;
+		this.pinnedChildren = pinnedChildren;
+	}
+
+	invalidate() {}
+
+	render(width) {
+		const flowLines = this.flowChildren.flatMap((child) => child.render(width));
+		const pinnedLines = this.pinnedChildren.flatMap((child) => child.render(width));
+		const spacerRows = Math.max(0, this.tui.terminal.rows - flowLines.length - pinnedLines.length);
+		return [...flowLines, ...Array.from({ length: spacerRows }, () => ""), ...pinnedLines];
+	}
+}
+
+const plain = (value) => value;
+const theme = {
+	borderColor: plain,
+	selectList: {
+		selectedPrefix: plain,
+		selectedText: plain,
+		description: plain,
+		scrollInfo: plain,
+		noMatch: plain,
+	},
+};
+const provider = {
+	triggerCharacters: ["/"],
+	async getSuggestions() {
+		return {
+			prefix: "/",
+			items: Array.from({ length: 8 }, (_, index) => ({
+				value: `cmd${index}`,
+				label: `/cmd${index}`,
+				description: `description ${index}`,
+			})),
+		};
+	},
+	applyCompletion(_lines, _line, _col, item) {
+		return { lines: [item.value], cursorLine: 0, cursorCol: item.value.length };
+	},
+};
+
+async function waitUntil(predicate, description) {
+	const deadline = Date.now() + 1000;
+	while (Date.now() < deadline) {
+		await new Promise((resolve) => setTimeout(resolve, 10));
+		if (predicate()) return;
+	}
+	assert.fail(`timed out waiting for ${description}`);
+}
+
+const terminal = new VirtualTerminal(50, 10);
+const tui = new TUI(terminal);
+const editor = new Editor(tui, theme, { autocompleteMaxVisible: 5 });
+editor.setAutocompleteProvider(provider);
+tui.addChild(new BottomLayout(tui, [new Lines(["chat"])], [editor, new Lines(["footer"])]));
+tui.setFocus(editor);
+tui.start();
+await terminal.waitForRender();
+terminal.sendInput("/");
+await waitUntil(() => editor.autocompleteState !== null, "autocomplete to open");
+await waitUntil(() => tui.previousLines.length === 11, "open autocomplete render");
+await terminal.waitForRender();
+terminal.sendInput("\x1b");
+await waitUntil(() => editor.autocompleteState === null, "autocomplete to close");
+await waitUntil(() => tui.previousLines.length === 10, "closed autocomplete render");
+await terminal.waitForRender();
+
+const viewport = terminal.getViewport();
+tui.stop();
+const trimmed = viewport.map((line) => line.trimEnd());
+assert.equal(trimmed.at(-1), "footer", `footer should return to the bottom row after autocomplete closes\n${trimmed.map((line, index) => `${index}: ${JSON.stringify(line)}`).join("\n")}`);
+assert.equal(trimmed[0], "chat", `chat line should be visible at the top of the bottom-aligned layout\n${trimmed.map((line, index) => `${index}: ${JSON.stringify(line)}`).join("\n")}`);
+JS
+
+PI_PACKAGE="$pi_package" nix shell nixpkgs#nodejs_22 -c node "$tmpdir/autocomplete-bottom-alignment.mjs"