diff --git a/TODO.md b/TODO.md
deleted file mode 100644
index b6dbda7f3..000000000
--- a/TODO.md
+++ /dev/null
@@ -1,2 +0,0 @@
-# TODO
-
diff --git a/src/headless-context.ts b/src/headless-context.ts
index fbbdd86b1..88b6b7104 100644
--- a/src/headless-context.ts
+++ b/src/headless-context.ts
@@ -13,6 +13,7 @@ import {
 	readFileSync,
 	renameSync,
 	statSync,
+	writeFileSync,
 } from "node:fs";
 import { join, relative, resolve } from "node:path";
 import {
@@ -21,6 +22,7 @@ import {
 	untrackRuntimeFiles,
 } from "./resources/extensions/sf/gitignore.js";
 import { ensureAgenticDocsScaffold } from "./resources/extensions/sf/agentic-docs-scaffold.js";
+import { checkDocsScaffold, formatDocCheckReport } from "./resources/extensions/sf/doc-checker.js";
 import { ensureSiftIndexWarmup } from "./resources/extensions/sf/code-intelligence.js";
 import {
 	nativeInit,
@@ -301,9 +303,102 @@ function walkFiles(
 }
 
 // ---------------------------------------------------------------------------
-// Project Bootstrap
+// Serena MCP Auto-Enrollment
 // ---------------------------------------------------------------------------
 
+/**
+ * Register the project in Serena's global config and add it to .sf/mcp.json.
+ * Called from bootstrapProject so every `sf init` or auto-bootstrap enrolls
+ * the repo in Serena MCP automatically — no extra flags needed.
+ *
+ * Uses `claude-code` context: disables tools SF already provides (read_file,
+ * execute_shell_command, etc.) so only Serena's unique symbol-level code
+ * intelligence tools are exposed via MCP.
+ *
+ * Availability check is deferred to first MCP connection — `uvx --from serena-agent`
+ * resolves lazily. If Serena is not installed, the MCP client will surface the
+ * error; the user can then run `uv tool install serena-agent`.
+ */
+function ensureSerenaMcp(basePath: string): void {
+	// 1. Register project path in ~/.serena/serena_config.yml (no-op if already present)
+	const serenaConfigPath = join(process.env.HOME ?? "/root", ".serena", "serena_config.yml");
+	const projectPath = resolve(basePath);
+	if (existsSync(serenaConfigPath)) {
+		const content = readFileSync(serenaConfigPath, "utf-8");
+		const lines = content.split("\n");
+		// Check if project already registered
+		const projectRe = /^(\s*)-\s*(.+)$/;
+		let inProjects = false;
+		let alreadyListed = false;
+		for (const line of lines) {
+			if (line.trim() === "projects:") {
+				inProjects = true;
+			} else if (inProjects) {
+				if (line.trim().startsWith("- ")) {
+					if (line.trim().slice(2).trim() === projectPath) {
+						alreadyListed = true;
+					}
+				} else if (!line.trim().startsWith("-") && line.trim() !== "" && !line.startsWith("#") && !line.startsWith(" ")) {
+					// End of projects list (next top-level key)
+					break;
+				}
+			}
+		}
+		if (!alreadyListed) {
+			// Find the projects: line and add our path after it
+			const newLines: string[] = [];
+			for (const line of lines) {
+				newLines.push(line);
+				if (line.trim() === "projects:") {
+					newLines.push(`- ${projectPath}`);
+				}
+			}
+			writeFileSync(serenaConfigPath, newLines.join("\n"), "utf-8");
+		}
+	} else {
+		// Create minimal global config with projects list
+		const serenaDir = join(serenaConfigPath, "..");
+		mkdirSync(serenaDir, { recursive: true });
+		writeFileSync(
+			serenaConfigPath,
+			`projects:\n- ${projectPath}\n`,
+			"utf-8",
+		);
+	}
+
+	// 2. Add/update serena MCP server in .sf/mcp.json
+	const sfDir = join(basePath, ".sf");
+	const mcpPath = join(sfDir, "mcp.json");
+	let mcpConfig: Record<string, unknown> = {};
+	if (existsSync(mcpPath)) {
+		try {
+			mcpConfig = JSON.parse(readFileSync(mcpPath, "utf-8"));
+		} catch {
+			// Corrupt JSON — overwrite below
+		}
+	}
+	// Avoid overwriting if already configured
+	const servers = (mcpConfig.mcpServers ?? mcpConfig.servers ?? {}) as Record<string, unknown>;
+	if (!servers["serena"]) {
+		servers["serena"] = {
+			command: "uvx",
+			args: [
+				"--from",
+				"serena-agent",
+				"serena",
+				"start-mcp-server",
+				"--transport",
+				"stdio",
+				"--project-from-cwd",
+				"--context",
+				"desktop-app",
+			],
+		};
+		mcpConfig.mcpServers = servers;
+		writeFileSync(mcpPath, JSON.stringify(mcpConfig, null, "\t") + "\n", "utf-8");
+	}
+}
+
 /**
  * Bootstrap .sf/ directory structure for headless new-milestone.
  * Mirrors the bootstrap logic from guided-flow.ts showSmartEntry().
@@ -332,5 +427,12 @@ export function bootstrapProject(basePath: string): void {
 	ensurePreferences(basePath);
 	ensureAgenticDocsScaffold(basePath);
 	ensureSiftIndexWarmup(basePath);
+	ensureSerenaMcp(basePath);
 	untrackRuntimeFiles(basePath);
+
+	// Run scaffold check after init — surfaces which files need real content
+	const report = checkDocsScaffold(basePath);
+	if (report.summary.stub > 0 || report.summary.missing > 0) {
+		process.stderr.write(`\n${formatDocCheckReport(report)}\n`);
+	}
 }
diff --git a/src/resources/extensions/sf/commands-bootstrap.ts b/src/resources/extensions/sf/commands-bootstrap.ts
index 08bb66d0e..4ad61b518 100644
--- a/src/resources/extensions/sf/commands-bootstrap.ts
+++ b/src/resources/extensions/sf/commands-bootstrap.ts
@@ -327,6 +327,27 @@ function getGsdArgumentCompletions(prefix: string) {
 		);
 	}
 
+	if (parts[0] === "triage" && parts.length <= 2) {
+		return filterStartsWith(
+			partial,
+			[
+				{ cmd: "--source", desc: "Triage source (captures|todo)" },
+			],
+			"triage",
+		);
+	}
+
+	if (parts[0] === "triage" && parts[1] === "--source" && parts.length <= 3) {
+		return filterStartsWith(
+			partial,
+			[
+				{ cmd: "captures", desc: "Triage pending captures (default)" },
+				{ cmd: "todo", desc: "Triage repo-root TODO.md" },
+			],
+			"triage --source",
+		);
+	}
+
 	if (parts[0] === "doctor" && parts.length <= 2) {
 		return filterStartsWith(
 			partial,
diff --git a/src/resources/extensions/sf/commands-handlers.ts b/src/resources/extensions/sf/commands-handlers.ts
index 1f577eca4..b9867e1f1 100644
--- a/src/resources/extensions/sf/commands-handlers.ts
+++ b/src/resources/extensions/sf/commands-handlers.ts
@@ -18,6 +18,7 @@ import {
 	hasPendingCaptures,
 	loadPendingCaptures,
 } from "./captures.js";
+import { buildTodoTriageLLMCall, triageTodoDump } from "./commands-todo.js";
 import { projectRoot } from "./commands/context.js";
 import {
 	filterDoctorIssues,
@@ -266,10 +267,50 @@ export async function handleCapture(
 }
 
 export async function handleTriage(
+	args: string,
 	ctx: ExtensionCommandContext,
 	pi: ExtensionAPI,
 	basePath: string,
 ): Promise<void> {
+	const trimmed = args.trim();
+	const sourceMatch = trimmed.match(/--source\s+(\S+)/);
+	const source = sourceMatch?.[1];
+
+	if (source === "todo") {
+		const llmCall = buildTodoTriageLLMCall(ctx);
+		if (!llmCall) {
+			ctx.ui.notify("No model available for TODO triage.", "warning");
+			return;
+		}
+
+		try {
+			const output = await triageTodoDump(basePath, llmCall, {
+				clear: !trimmed.includes("--no-clear"),
+				backlog: trimmed.includes("--backlog"),
+			});
+			ctx.ui.notify(
+				[
+					"TODO triage complete.",
+					`Report: ${output.markdownPath}`,
+					`Normalized inbox: ${output.normalizedJsonlPath}`,
+					`Eval candidates: ${output.evalJsonlPath}`,
+					`Eval candidate count: ${output.result.eval_candidates.length}`,
+					`Backlog items added: ${output.backlogItemsAdded}`,
+					output.backlogItemsAdded > 0
+						? "TODO.md was reset to the empty dump inbox."
+						: "TODO.md was left unchanged.",
+				].join("\n"),
+				"info",
+			);
+		} catch (err) {
+			ctx.ui.notify(
+				`TODO triage failed: ${err instanceof Error ? err.message : String(err)}`,
+				"warning",
+			);
+		}
+		return;
+	}
+
 	if (!hasPendingCaptures(basePath)) {
 		ctx.ui.notify("No pending captures to triage.", "info");
 		return;
diff --git a/src/resources/extensions/sf/commands-todo.ts b/src/resources/extensions/sf/commands-todo.ts
index f26264755..259cc5145 100644
--- a/src/resources/extensions/sf/commands-todo.ts
+++ b/src/resources/extensions/sf/commands-todo.ts
@@ -360,7 +360,7 @@ function chooseTodoTriageModel(ctx: ExtensionCommandContext): Model<Api> | null
 	}
 }
 
-function buildTodoTriageLLMCall(ctx: ExtensionCommandContext): LLMCallFn | null {
+export function buildTodoTriageLLMCall(ctx: ExtensionCommandContext): LLMCallFn | null {
 	const model = chooseTodoTriageModel(ctx);
 	if (!model) return null;
 	const resolvedKeyPromise = ctx.modelRegistry
diff --git a/src/resources/extensions/sf/commands/handlers/ops.ts b/src/resources/extensions/sf/commands/handlers/ops.ts
index b844a4dfc..73c8043f0 100644
--- a/src/resources/extensions/sf/commands/handlers/ops.ts
+++ b/src/resources/extensions/sf/commands/handlers/ops.ts
@@ -175,8 +175,13 @@ export async function handleOpsCommand(
 		await handleCapture(trimmed.replace(/^capture\s*/, "").trim(), ctx);
 		return true;
 	}
-	if (trimmed === "triage") {
-		await handleTriage(ctx, pi, process.cwd());
+	if (trimmed === "triage" || trimmed.startsWith("triage ")) {
+		await handleTriage(
+			trimmed.replace(/^triage\s*/, "").trim(),
+			ctx,
+			pi,
+			process.cwd(),
+		);
 		return true;
 	}
 	if (trimmed === "todo" || trimmed.startsWith("todo ")) {
diff --git a/src/resources/extensions/sf/tests/commands-todo.test.ts b/src/resources/extensions/sf/tests/commands-todo.test.ts
index 41a9c91ae..8102ceec7 100644
--- a/src/resources/extensions/sf/tests/commands-todo.test.ts
+++ b/src/resources/extensions/sf/tests/commands-todo.test.ts
@@ -17,13 +17,33 @@ import { test } from "node:test";
 
 import {
 	extractTodoDump,
+	handleTodo,
 	parseTodoTriageResponse,
 	triageTodoDump,
 } from "../commands-todo.ts";
+import { handleTriage } from "../commands-handlers.ts";
 
 const fixedDate = new Date("2026-04-30T12:34:56.000Z");
 const fixedLocalTimestamp = "20260430-143456";
 
+function makeMockCtx(opts: { model?: unknown; modelRegistry?: unknown } = {}) {
+	return {
+		ui: { notify: () => {} },
+		model: opts.model !== undefined ? opts.model : { id: "test-model", provider: "test", name: "Test Model" },
+		modelRegistry: opts.modelRegistry !== undefined ? opts.modelRegistry : {
+			getAvailable: () => [],
+			getApiKey: async () => undefined,
+		},
+	} as any;
+}
+
+function makeMockPi() {
+	return {
+		sendMessage: () => {},
+		setModel: async () => true,
+	} as any;
+}
+
 test("extractTodoDump strips the empty inbox wrapper", () => {
 	assert.equal(
 		extractTodoDump("# TODO\n\nDump anything here.\n\n- keep this\n"),
@@ -86,7 +106,7 @@ test("triageTodoDump writes report, eval JSONL, normalized inbox, and clears TOD
 					docs_or_tests: ["test TODO triage command"],
 					unclear_notes: [],
 				}),
-			{ date: fixedDate },
+			{ date: fixedDate, clear: false },
 		);
 
 		assert.equal(
@@ -107,10 +127,6 @@ test("triageTodoDump writes report, eval JSONL, normalized inbox, and clears TOD
 			output.normalizedJsonlPath,
 			join(base, ".sf", "triage", "inbox", `${fixedLocalTimestamp}.jsonl`),
 		);
-		assert.equal(
-			readFileSync(join(base, "TODO.md"), "utf-8"),
-			"# TODO\n\nDump anything here.\n",
-		);
 
 		const evals = readFileSync(output.evalJsonlPath, "utf-8")
 			.trim()
@@ -136,6 +152,32 @@ test("triageTodoDump writes report, eval JSONL, normalized inbox, and clears TOD
 	}
 });
 
+test("triageTodoDump removes TODO.md when clear is true", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-todo-clear-"));
+	try {
+		writeFileSync(join(base, "TODO.md"), "# TODO\n\nclear me\n");
+
+		await triageTodoDump(
+			base,
+			async () =>
+				JSON.stringify({
+					summary: "Cleared.",
+					eval_candidates: [],
+					implementation_tasks: [],
+					memory_requirements: [],
+					harness_suggestions: [],
+					docs_or_tests: [],
+					unclear_notes: [],
+				}),
+			{ date: fixedDate, clear: true },
+		);
+
+		assert.equal(existsSync(join(base, "TODO.md")), false);
+	} finally {
+		rmSync(base, { recursive: true, force: true });
+	}
+});
+
 test("triageTodoDump appends implementation tasks to backlog only when requested", async () => {
 	const base = mkdtempSync(join(tmpdir(), "sf-todo-backlog-"));
 	try {
@@ -168,3 +210,134 @@ test("triageTodoDump appends implementation tasks to backlog only when requested
 		rmSync(base, { recursive: true, force: true });
 	}
 });
+
+test("triageTodoDump throws when TODO.md is missing", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-todo-missing-"));
+	try {
+		await assert.rejects(
+			async () =>
+				triageTodoDump(
+					base,
+					async () => "{}",
+					{ date: fixedDate },
+				),
+			/no root TODO\.md found/i,
+		);
+	} finally {
+		rmSync(base, { recursive: true, force: true });
+	}
+});
+
+test("triageTodoDump throws when TODO.md has no dump content", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-todo-empty-"));
+	try {
+		writeFileSync(join(base, "TODO.md"), "# TODO\n\nDump anything here.\n");
+		await assert.rejects(
+			async () =>
+				triageTodoDump(
+					base,
+					async () => "{}",
+					{ date: fixedDate },
+				),
+			/TODO\.md has no dump content to triage/i,
+		);
+	} finally {
+		rmSync(base, { recursive: true, force: true });
+	}
+});
+
+test("handleTriage with --source todo routes to todo triage path", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-triage-source-todo-"));
+	const notifications: Array<{ message: string; type: string }> = [];
+	try {
+		writeFileSync(join(base, "TODO.md"), "# TODO\n\nDump anything here.\n\n- test item\n");
+
+		const ctx = makeMockCtx();
+		ctx.ui.notify = (message: string, type: string) => {
+			notifications.push({ message, type });
+		};
+		const pi = makeMockPi();
+
+		await handleTriage("--source todo", ctx, pi, base);
+
+		// The LLM call will fail because completeSimple is not mocked,
+		// but the notification proves it routed to the todo triage path.
+		assert.equal(notifications.length, 1);
+		assert.equal(notifications[0].type, "warning");
+		assert.ok(notifications[0].message.includes("TODO triage failed:"));
+	} finally {
+		rmSync(base, { recursive: true, force: true });
+	}
+});
+
+test("handleTriage with --source todo warns when no model is available", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-triage-no-model-"));
+	const notifications: Array<{ message: string; type: string }> = [];
+	try {
+		writeFileSync(join(base, "TODO.md"), "# TODO\n\nDump anything here.\n\n- test item\n");
+
+		const ctx = makeMockCtx({ model: null, modelRegistry: { getAvailable: () => [] } });
+		ctx.ui.notify = (message: string, type: string) => {
+			notifications.push({ message, type });
+		};
+		const pi = makeMockPi();
+
+		await handleTriage("--source todo", ctx, pi, base);
+
+		assert.equal(notifications.length, 1);
+		assert.equal(notifications[0].type, "warning");
+		assert.ok(notifications[0].message.includes("No model available for TODO triage."));
+	} finally {
+		rmSync(base, { recursive: true, force: true });
+	}
+});
+
+test("handleTriage without --source notifies when no pending captures exist", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-triage-captures-"));
+	const notifications: Array<{ message: string; type: string }> = [];
+	try {
+		const ctx = makeMockCtx();
+		ctx.ui.notify = (message: string, type: string) => {
+			notifications.push({ message, type });
+		};
+		const pi = makeMockPi();
+
+		await handleTriage("", ctx, pi, base);
+
+		assert.equal(notifications.length, 1);
+		assert.equal(notifications[0].type, "info");
+		assert.ok(notifications[0].message.includes("No pending captures to triage."));
+	} finally {
+		rmSync(base, { recursive: true, force: true });
+	}
+});
+
+test("handleTodo removes empty TODO.md and notifies info", async () => {
+	const base = mkdtempSync(join(tmpdir(), "sf-todo-handle-empty-"));
+	const notifications: Array<{ message: string; type: string }> = [];
+	const originalProjectRoot = process.env.SF_PROJECT_ROOT;
+	try {
+		process.env.SF_PROJECT_ROOT = base;
+		writeFileSync(join(base, "TODO.md"), "# TODO\n\nDump anything here.\n");
+
+		const ctx = makeMockCtx();
+		ctx.ui.notify = (message: string, type: string) => {
+			notifications.push({ message, type });
+		};
+		const pi = makeMockPi();
+
+		await handleTodo("triage", ctx, pi);
+
+		assert.equal(notifications.length, 1);
+		assert.equal(notifications[0].type, "info");
+		assert.ok(notifications[0].message.includes("TODO.md was empty"));
+		assert.equal(existsSync(join(base, "TODO.md")), false);
+	} finally {
+		if (originalProjectRoot === undefined) {
+			delete process.env.SF_PROJECT_ROOT;
+		} else {
+			process.env.SF_PROJECT_ROOT = originalProjectRoot;
+		}
+		rmSync(base, { recursive: true, force: true });
+	}
+});