fix: reduce stale doctor warnings

src/resources/extensions/sf/doctor-engine-checks.js

@@ -1,7 +1,12 @@
 import { existsSync, readdirSync, renameSync, rmSync, statSync } from "node:fs";
 import { join } from "node:path";
 import { milestonesDir, resolveMilestoneFile } from "./paths.js";
-import { _getAdapter, getAllMilestones, isDbAvailable } from "./sf-db.js";
+import {
+	_getAdapter,
+	getAllMilestones,
+	isDbAvailable,
+	openDatabase,
+} from "./sf-db.js";
 import { deriveState } from "./state.js";
 import { readEvents } from "./workflow-events.js";
 import { renderAllProjections } from "./workflow-projections.js";
@@ -28,18 +33,17 @@ function normalizeLegacyDirectory(
 	const sourcePath = join(parentDir, entry);
 	const targetPath = join(parentDir, bareId);
 	const conflict = existsSync(targetPath);
+	if (conflict) return;
 	issues.push({
-		severity: conflict ? "warning" : "info",
+		severity: "info",
 		code: "legacy_plan_slug_directory",
 		scope: "project",
 		unitId: `${unitPrefix}/${entry}`,
-		message: conflict
-			? `Legacy plan directory ${sourcePath} should be renamed to ${targetPath}, but the target already exists. Merge manually before running doctor fix.`
-			: `Legacy plan directory ${sourcePath} should be renamed to bare ID directory ${targetPath}.`,
+		message: `Legacy plan directory ${sourcePath} should be renamed to bare ID directory ${targetPath}.`,
 		file: sourcePath,
-		fixable: !conflict,
+		fixable: true,
 	});
-	if (conflict || !shouldFix?.("legacy_plan_slug_directory")) return;
+	if (!shouldFix?.("legacy_plan_slug_directory")) return;
 	try {
 		renameSync(sourcePath, targetPath);
 		fixesApplied.push(
@@ -105,6 +109,14 @@ export async function checkEngineHealth(
 	shouldFix,
 ) {
 	const dbPath = join(basePath, ".sf", "sf.db");
+	if (!isDbAvailable() && existsSync(dbPath)) {
+		try {
+			openDatabase(dbPath);
+		} catch {
+			// Report below. Doctor must not throw just because the engine DB is
+			// locked, corrupt, or unavailable in this process.
+		}
+	}
 	if (!isDbAvailable() && existsSync(dbPath)) {
 		issues.push({
 			severity: "warning",

src/resources/extensions/sf/doctor-environment.js

@@ -543,7 +543,7 @@ function checkGitRemote(basePath) {
 	const remote = tryExec("git remote get-url origin", basePath);
 	if (!remote) return null;
 	// Quick connectivity check with short timeout
-	const result = tryExec("git ls-remote --exit-code -h origin HEAD", basePath);
+	const result = tryExec("git ls-remote --exit-code origin HEAD", basePath);
 	if (result === null) {
 		return {
 			name: "git_remote",

src/resources/extensions/sf/doctor-runtime-checks.js

@@ -704,8 +704,6 @@ function formatBucketCountParts(counts) {
 		parts.push(`${counts.upgradable} pending upgrade`);
 	if (counts["editing-drift"] && counts["editing-drift"] > 0)
 		parts.push(`${counts["editing-drift"]} editing-drift`);
-	if (counts.untracked && counts.untracked > 0)
-		parts.push(`${counts.untracked} untracked`);
 	const pendingCount = (counts.missing ?? 0) + (counts.upgradable ?? 0);
 	return { parts, pendingCount };
 }
@@ -727,10 +725,7 @@ export function checkScaffoldFreshness(basePath) {
 	}
 	const counts = report.countsByBucket;
 	const actionable =
-		counts.missing +
-		counts.upgradable +
-		counts["editing-drift"] +
-		counts.untracked;
+		counts.missing + counts.upgradable + counts["editing-drift"];
 	if (actionable === 0) return null;
 	const { parts, pendingCount } = formatBucketCountParts(counts);
 	const summary = parts.join(", ");

src/resources/extensions/sf/tests/agentic-docs-scaffold.test.mjs

@@ -9,7 +9,11 @@ import {
 import { tmpdir } from "node:os";
 import { dirname, join } from "node:path";
 import { afterEach, test } from "vitest";
-import { ensureAgenticDocsScaffold } from "../agentic-docs-scaffold.js";
+import {
+	ensureAgenticDocsScaffold,
+	SCAFFOLD_FILES,
+} from "../agentic-docs-scaffold.js";
+import { checkScaffoldFreshness } from "../doctor-runtime-checks.js";
 import { detectScaffoldDrift } from "../scaffold-drift.js";
 import { extractMarker, stampScaffoldFile } from "../scaffold-versioning.js";
 
@@ -131,3 +135,14 @@ All lines should start with \`OK:\` for the bootstrap spec to pass.
 	assert.equal(existsSync(join(root, "harness")), false);
 	assert.equal(existsSync(join(root, ".sf/harness/specs/bootstrap.md")), true);
 });
+
+test("checkScaffoldFreshness_when_only_markerless_scaffold_exists_does_not_warn", () => {
+	const root = makeProject();
+	for (const file of SCAFFOLD_FILES) {
+		const target = join(root, file.path);
+		mkdirSync(dirname(target), { recursive: true });
+		writeFileSync(target, file.content, "utf-8");
+	}
+
+	assert.equal(checkScaffoldFreshness(root), null);
+});

src/resources/extensions/sf/tests/doctor-plan-dir-normalization.test.mjs

@@ -9,7 +9,11 @@ import {
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { afterEach, describe, test } from "vitest";
-import { normalizeLegacyPlanSlugDirectories } from "../doctor-engine-checks.js";
+import {
+	checkEngineHealth,
+	normalizeLegacyPlanSlugDirectories,
+} from "../doctor-engine-checks.js";
+import { closeDatabase, openDatabase } from "../sf-db.js";
 
 const tmpDirs = [];
 
@@ -21,6 +25,7 @@ function makeProject() {
 }
 
 afterEach(() => {
+	closeDatabase();
 	while (tmpDirs.length > 0) {
 		const dir = tmpDirs.pop();
 		if (dir) rmSync(dir, { recursive: true, force: true });
@@ -96,15 +101,31 @@ describe("doctor plan directory normalization", () => {
 			(code) => code === "legacy_plan_slug_directory",
 		);
 
-		const issue = issues.find(
-			(candidate) => candidate.code === "legacy_plan_slug_directory",
+		assert.equal(
+			issues.some(
+				(candidate) => candidate.code === "legacy_plan_slug_directory",
+			),
+			false,
 		);
-		assert.equal(issue?.fixable, false);
-		assert.match(issue?.message ?? "", /target already exists/);
 		assert.equal(
 			existsSync(join(project, ".sf", "milestones", "M001-long-name")),
 			true,
 		);
 		assert.deepEqual(fixesApplied, []);
 	});
+
+	test("checkEngineHealth_when_db_file_can_open_does_not_report_unavailable", async () => {
+		const project = makeProject();
+		const dbPath = join(project, ".sf", "sf.db");
+		assert.equal(openDatabase(dbPath), true);
+		closeDatabase();
+		const issues = [];
+
+		await checkEngineHealth(project, issues, [], () => false);
+
+		assert.equal(
+			issues.some((issue) => issue.code === "db_unavailable"),
+			false,
+		);
+	});
 });