diff --git a/docs/dev/generated-artifact-policy.md b/docs/dev/generated-artifact-policy.md
new file mode 100644
index 000000000..235bbd3f8
--- /dev/null
+++ b/docs/dev/generated-artifact-policy.md
@@ -0,0 +1,35 @@
+# Generated Artifact Policy
+
+SF keeps operational generated artifacts out of the project root unless a human
+explicitly promotes them into durable project documentation.
+
+## Default Locations
+
+- `.sf/` stores SF-local operational state, generated harness notes, scaffold
+  manifests, runtime caches, locks, and temporary agent files.
+- `docs/plans/`, `docs/specs/`, and `docs/adr/` store promoted, reviewed,
+  durable project artifacts.
+- Root files such as `AGENTS.md`, `ARCHITECTURE.md`, and `.siftignore` are
+  allowed only when they are part of the versioned scaffold contract.
+
+## Harness
+
+Generated harness material belongs under `.sf/harness/`.
+
+Top-level `harness/` is not created by SF by default. If a project intentionally
+owns a top-level harness, SF leaves it alone unless the files still carry
+pending `sf-doc` markers proving they are old SF-generated residue.
+
+## Doctor Cleanup
+
+`/sf doctor --fix` may remove root-level generated residue only when all of the
+following are true:
+
+- the file is under a legacy SF-generated path such as `harness/specs/`;
+- the file has an `sf-doc` marker;
+- the marker template matches the file path;
+- the marker state is `pending`;
+- the current body hash still matches the marker hash.
+
+Anything edited, completed, unmarked, or project-owned is reported conservatively
+or left untouched.
diff --git a/src/resources/extensions/sf/doctor.js b/src/resources/extensions/sf/doctor.js
index 94e480792..e657d6486 100644
--- a/src/resources/extensions/sf/doctor.js
+++ b/src/resources/extensions/sf/doctor.js
@@ -4,8 +4,9 @@ import {
 	mkdirSync,
 	readdirSync,
 	readFileSync,
+	rmSync,
 } from "node:fs";
-import { join } from "node:path";
+import { dirname, join } from "node:path";
 import { invalidateAllCaches } from "./cache.js";
 import {
 	checkEngineHealth,
@@ -42,6 +43,7 @@ import {
 	sfRoot,
 } from "./paths.js";
 import { loadEffectiveSFPreferences } from "./preferences.js";
+import { bodyHash, extractMarker } from "./scaffold-versioning.js";
 import { readAllSelfFeedback, recordSelfFeedback } from "./self-feedback.js";
 import { getMilestoneSlices, getSliceTasks, isDbAvailable } from "./sf-db.js";
 import { deriveState, isMilestoneComplete } from "./state.js";
@@ -53,6 +55,79 @@ const DEFAULT_STALE_PROGRESS_MS = 20 * 60 * 1000;
 const DEFAULT_OPTIONAL_CHILD_BUDGET_MS = 30 * 60 * 1000;
 const REPEATED_FAILURE_THRESHOLD = 3;
 const FLOW_AUDIT_ROLLUP_KIND = "flow-audit:repeated-milestone-failure";
+const LEGACY_ROOT_HARNESS_PATHS = [
+	"harness/AGENTS.md",
+	"harness/specs/AGENTS.md",
+	"harness/specs/bootstrap.md",
+	"harness/evals/AGENTS.md",
+	"harness/graders/AGENTS.md",
+];
+
+function pruneEmptyDir(path) {
+	try {
+		if (existsSync(path) && readdirSync(path).length === 0) {
+			rmSync(path, { recursive: false });
+		}
+	} catch {
+		// Best-effort cleanup only.
+	}
+}
+
+function collectOwnedLegacyRootHarnessFiles(basePath) {
+	const owned = [];
+	for (const relPath of LEGACY_ROOT_HARNESS_PATHS) {
+		const target = join(basePath, relPath);
+		if (!existsSync(target)) continue;
+		const { marker, body } = extractMarker(target);
+		if (!marker) continue;
+		if (marker.template !== relPath) continue;
+		if (marker.state !== "pending") continue;
+		if (bodyHash(body) !== marker.hash) continue;
+		owned.push(relPath);
+	}
+	return owned;
+}
+
+function removeOwnedLegacyRootHarnessFiles(basePath, relPaths) {
+	for (const relPath of relPaths) {
+		rmSync(join(basePath, relPath), { force: true });
+	}
+	for (const relPath of relPaths) {
+		let dir = dirname(join(basePath, relPath));
+		while (dir.startsWith(join(basePath, "harness"))) {
+			pruneEmptyDir(dir);
+			if (dir === join(basePath, "harness")) break;
+			dir = dirname(dir);
+		}
+	}
+	pruneEmptyDir(join(basePath, "harness"));
+}
+
+function checkGeneratedArtifactResidue(
+	basePath,
+	issues,
+	fixesApplied,
+	shouldFix,
+) {
+	const ownedRootHarness = collectOwnedLegacyRootHarnessFiles(basePath);
+	if (ownedRootHarness.length === 0) return;
+	issues.push({
+		severity: "warning",
+		code: "generated_root_harness_residue",
+		scope: "project",
+		unitId: "project",
+		message: `Found ${ownedRootHarness.length} SF-owned generated harness file(s) under root harness/. Generated operational harness belongs under .sf/harness/; promote durable contracts to docs/specs/ explicitly.`,
+		file: "harness/",
+		fixable: true,
+	});
+	if (shouldFix("generated_root_harness_residue")) {
+		removeOwnedLegacyRootHarnessFiles(basePath, ownedRootHarness);
+		fixesApplied.push(
+			`removed ${ownedRootHarness.length} SF-owned root harness file(s)`,
+		);
+	}
+}
+
 function parseEpochMs(value, fallbackMs) {
 	if (typeof value === "number" && Number.isFinite(value)) {
 		return value < 10_000_000_000 ? value * 1000 : value;
@@ -1024,6 +1099,7 @@ export async function runSFDoctor(basePath, options) {
 			});
 		}
 	}
+	checkGeneratedArtifactResidue(basePath, issues, fixesApplied, shouldFix);
 	// Git health checks — timed
 	const t0git = Date.now();
 	const isolationMode =
diff --git a/src/resources/extensions/sf/tests/doctor-generated-artifacts.test.mjs b/src/resources/extensions/sf/tests/doctor-generated-artifacts.test.mjs
new file mode 100644
index 000000000..0f215abbe
--- /dev/null
+++ b/src/resources/extensions/sf/tests/doctor-generated-artifacts.test.mjs
@@ -0,0 +1,91 @@
+import assert from "node:assert/strict";
+import {
+	existsSync,
+	mkdirSync,
+	mkdtempSync,
+	rmSync,
+	writeFileSync,
+} from "node:fs";
+import { tmpdir } from "node:os";
+import { dirname, join } from "node:path";
+import { afterEach, describe, test } from "vitest";
+import { runSFDoctor } from "../doctor.js";
+import { stampScaffoldFile } from "../scaffold-versioning.js";
+
+const tmpDirs = [];
+
+afterEach(() => {
+	while (tmpDirs.length > 0) {
+		const dir = tmpDirs.pop();
+		if (dir) rmSync(dir, { recursive: true, force: true });
+	}
+});
+
+function makeProject() {
+	const dir = mkdtempSync(join(tmpdir(), "sf-doctor-generated-"));
+	tmpDirs.push(dir);
+	mkdirSync(join(dir, ".sf"), { recursive: true });
+	return dir;
+}
+
+function writeOwnedLegacyHarnessFile(root, relPath) {
+	const target = join(root, relPath);
+	mkdirSync(dirname(target), { recursive: true });
+	writeFileSync(target, `# ${relPath}\n`, "utf-8");
+	stampScaffoldFile(target, relPath, "2.75.0", "pending");
+}
+
+describe("doctor generated artifact hygiene", () => {
+	test("runSFDoctor_reports_sf_owned_root_harness_residue", async () => {
+		const project = makeProject();
+		writeOwnedLegacyHarnessFile(project, "harness/specs/bootstrap.md");
+
+		const report = await runSFDoctor(project, { scope: "project" });
+
+		const issue = report.issues.find(
+			(i) => i.code === "generated_root_harness_residue",
+		);
+		assert.equal(issue?.fixable, true);
+		assert.equal(existsSync(join(project, "harness/specs/bootstrap.md")), true);
+	});
+
+	test("runSFDoctor_fix_removes_only_sf_owned_pending_root_harness", async () => {
+		const project = makeProject();
+		writeOwnedLegacyHarnessFile(project, "harness/specs/bootstrap.md");
+
+		const report = await runSFDoctor(project, {
+			fix: true,
+			fixLevel: "all",
+			scope: "project",
+		});
+
+		assert.ok(
+			report.fixesApplied.includes("removed 1 SF-owned root harness file(s)"),
+		);
+		assert.equal(existsSync(join(project, "harness")), false);
+	});
+
+	test("runSFDoctor_ignores_user_owned_root_harness", async () => {
+		const project = makeProject();
+		mkdirSync(join(project, "harness/specs"), { recursive: true });
+		writeFileSync(
+			join(project, "harness/specs/project-contract.md"),
+			"# Project-owned harness\n",
+		);
+
+		const report = await runSFDoctor(project, {
+			fix: true,
+			fixLevel: "all",
+			scope: "project",
+		});
+
+		assert.equal(
+			report.issues.some((i) => i.code === "generated_root_harness_residue"),
+			false,
+		);
+		assert.equal(
+			existsSync(join(project, "harness/specs/project-contract.md")),
+			true,
+		);
+	});
+});