fix: make doctor repair sf form drift

flake.nix

@@ -23,9 +23,7 @@
           clippy
           git
           just
-          nodejs_24
           pkg-config
-          nodePackages.typescript
           protobuf
           rust-analyzer
           rustc
@@ -36,6 +34,12 @@
 
         shellHook = ''
           export SF_SOURCE_DIR="${toString ./.}"
+          if [ -x "$HOME/.local/bin/mise" ]; then
+            MISE_NODE_BIN="$("$HOME/.local/bin/mise" which node 2>/dev/null || true)"
+            if [ -n "$MISE_NODE_BIN" ]; then
+              export PATH="$(dirname "$MISE_NODE_BIN"):$PATH"
+            fi
+          fi
           export PATH="$SF_SOURCE_DIR/bin:$PATH"
           export RUST_BACKTRACE=1
 

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

@@ -312,8 +312,12 @@ export async function checkRuntimeHealth(
 	// ── Gitignore drift ───────────────────────────────────────────────────
 	try {
 		const gitignorePath = join(basePath, ".gitignore");
+		const excludePath = join(basePath, ".git", "info", "exclude");
 		if (existsSync(gitignorePath) && nativeIsRepo(basePath)) {
-			const content = readFileSync(gitignorePath, "utf-8");
+			const content = [
+				readFileSync(gitignorePath, "utf-8"),
+				existsSync(excludePath) ? readFileSync(excludePath, "utf-8") : "",
+			].join("\n");
 			const existingLines = new Set(
 				content
 					.split("\n")
@@ -334,8 +338,8 @@ export async function checkRuntimeHealth(
 						code: "gitignore_missing_patterns",
 						scope: "project",
 						unitId: "project",
-						message: `${missing.length} critical SF runtime pattern(s) missing from .gitignore: ${missing.join(", ")}`,
-						file: ".gitignore",
+						message: `${missing.length} critical SF runtime pattern(s) missing from .gitignore or .git/info/exclude: ${missing.join(", ")}`,
+						file: ".git/info/exclude",
 						fixable: true,
 					});
 					if (shouldFix("gitignore_missing_patterns")) {

src/resources/extensions/sf/doctor.js

@@ -203,6 +203,68 @@ function parseMarkdownFrontmatter(content) {
 	}
 }
 
+function normalizeFrontmatterArrayScalars(frontmatter) {
+	const lines = frontmatter.split("\n");
+	const output = [];
+	for (let i = 0; i < lines.length; i++) {
+		const line = lines[i];
+		const itemMatch = line.match(/^(\s*)-\s+(.+)$/);
+		if (!itemMatch) {
+			output.push(line);
+			continue;
+		}
+		const indent = itemMatch[1];
+		const continuation = [itemMatch[2]];
+		while (i + 1 < lines.length) {
+			const next = lines[i + 1];
+			if (/^\S[^:]*:\s*/.test(next)) break;
+			if (next.match(/^(\s*)-\s+(.+)$/)?.[1] === indent) break;
+			if (next.trim() === "") break;
+			continuation.push(next.trim());
+			i++;
+		}
+		output.push(`${indent}- ${JSON.stringify(continuation.join("\\n"))}`);
+	}
+	return output.join("\n");
+}
+
+function repairMarkdownFrontmatter(content) {
+	if (!content.startsWith("---\n") && !content.startsWith("---\r\n")) {
+		return null;
+	}
+	const normalized = content.replace(/\r\n/g, "\n");
+	const end = normalized.indexOf("\n---\n", 4);
+	if (end === -1) return null;
+	const frontmatter = normalized.slice(4, end);
+	const repairedFrontmatter = normalizeFrontmatterArrayScalars(frontmatter);
+	if (repairedFrontmatter === frontmatter) return null;
+	try {
+		parseYaml(repairedFrontmatter);
+	} catch {
+		return null;
+	}
+	return `---\n${repairedFrontmatter}\n---\n${normalized.slice(end + 5)}`;
+}
+
+function repairJsonl(content) {
+	if (!content.trim()) return null;
+	try {
+		const parsed = JSON.parse(content);
+		if (parsed && typeof parsed === "object") {
+			return `${JSON.stringify(parsed)}\n`;
+		}
+	} catch {
+		return null;
+	}
+	return null;
+}
+
+function repairSfFormContent(ext, content) {
+	if (ext === ".jsonl") return repairJsonl(content);
+	if (ext === ".md") return repairMarkdownFrontmatter(content);
+	return null;
+}
+
 function checkSfFormSyntax(basePath, issues, fixesApplied, shouldFix) {
 	const root = sfRoot(basePath);
 	for (const relPath of collectSfFormFiles(basePath)) {
@@ -229,6 +291,8 @@ function checkSfFormSyntax(basePath, issues, fixesApplied, shouldFix) {
 			parseError = error instanceof Error ? error.message : String(error);
 		}
 		if (parseError) {
+			const repaired = repairSfFormContent(ext, content);
+			const repairable = repaired !== null;
 			issues.push({
 				severity: "error",
 				code: "invalid_sf_form",
@@ -236,8 +300,13 @@ function checkSfFormSyntax(basePath, issues, fixesApplied, shouldFix) {
 				unitId: "project",
 				message: `.sf/${relPath} has invalid ${ext.slice(1) || "form"} syntax: ${parseError}`,
 				file: `.sf/${relPath}`,
-				fixable: false,
+				fixable: repairable,
 			});
+			if (repairable && shouldFix("invalid_sf_form")) {
+				writeFileSync(filePath, repaired, "utf-8");
+				content = repaired;
+				fixesApplied.push(`repaired .sf form syntax in .sf/${relPath}`);
+			}
 		}
 
 		if (

src/resources/extensions/sf/tests/doctor-sf-form-lint.test.mjs

@@ -79,4 +79,74 @@ describe("doctor .sf form lint", () => {
 			"# SF guidance\n\nSF owns this scaffold.\n",
 		);
 	});
+
+	test("runSFDoctor_fix_repairs_json_object_written_as_jsonl", async () => {
+		const project = makeProject();
+		const target = join(project, ".sf", "self-feedback-resolved.jsonl");
+		writeFileSync(
+			target,
+			'{\n  "id": "sf-test",\n  "resolvedAt": "2026-05-05T00:00:00.000Z"\n}\n',
+			"utf-8",
+		);
+
+		const report = await runSFDoctor(project, {
+			fix: true,
+			fixLevel: "all",
+			scope: "project",
+		});
+
+		assert.ok(
+			report.fixesApplied.includes(
+				"repaired .sf form syntax in .sf/self-feedback-resolved.jsonl",
+			),
+		);
+		assert.equal(
+			readFileSync(target, "utf-8"),
+			'{"id":"sf-test","resolvedAt":"2026-05-05T00:00:00.000Z"}\n',
+		);
+	});
+
+	test("runSFDoctor_fix_quotes_frontmatter_array_scalars_with_colons_and_newlines", async () => {
+		const project = makeProject();
+		const target = join(project, ".sf", "milestones", "M001", "SUMMARY.md");
+		mkdirSync(join(project, ".sf", "milestones", "M001"), {
+			recursive: true,
+		});
+		writeFileSync(
+			target,
+			[
+				"---",
+				"id: M001",
+				"key_decisions:",
+				"  - Fixed test with clear: false and clear: true cases.",
+				"  - Empty files contain one newline (not `[]",
+				"`) so split works.",
+				"---",
+				"# Summary",
+				"",
+			].join("\n"),
+			"utf-8",
+		);
+
+		const report = await runSFDoctor(project, {
+			fix: true,
+			fixLevel: "all",
+			scope: "project",
+		});
+
+		assert.ok(
+			report.fixesApplied.includes(
+				"repaired .sf form syntax in .sf/milestones/M001/SUMMARY.md",
+			),
+		);
+		const repaired = readFileSync(target, "utf-8");
+		assert.match(
+			repaired,
+			/ {2}- "Fixed test with clear: false and clear: true cases\."/,
+		);
+		assert.match(
+			repaired,
+			/ {2}- "Empty files contain one newline .*\\\\n.* so split works\."/,
+		);
+	});
 });