diff --git a/packages/coding-agent/src/discovery/github.ts b/packages/coding-agent/src/discovery/github.ts
index eed93d486..a19db3930 100644
--- a/packages/coding-agent/src/discovery/github.ts
+++ b/packages/coding-agent/src/discovery/github.ts
@@ -216,22 +216,16 @@ function transformInstructionRule(
 }
 
 function normalizeApplyToGlobs(value: unknown): string[] | undefined {
-	if (typeof value === "string") {
-		const glob = value.trim();
-		return glob ? [glob] : undefined;
-	}
-	if (!Array.isArray(value)) {
-		return undefined;
-	}
-	const globs = value
-		.filter((item): item is string => typeof item === "string")
-		.map(item => item.trim())
-		.filter(Boolean);
+	// GitHub documents applyTo as a single comma-separated string (e.g.
+	// "**/*.ts,**/*.tsx"); also tolerate a YAML array of such strings.
+	const raw = Array.isArray(value) ? value : [value];
+	const globs = raw.flatMap(item => (typeof item === "string" ? parseCSV(item) : []));
 	return globs.length > 0 ? globs : undefined;
 }
 
 function isAlwaysApplyGlob(glob: string): boolean {
-	return glob === "*" || glob === "**";
+	// GitHub treats "*", "**", and "**/*" as matching every file.
+	return glob === "*" || glob === "**" || glob === "**/*";
 }
 
 function describeInstructionRule(globs: string[] | undefined): string {
diff --git a/packages/coding-agent/test/discovery/github-copilot.test.ts b/packages/coding-agent/test/discovery/github-copilot.test.ts
index 846c282d5..e8b99618b 100644
--- a/packages/coding-agent/test/discovery/github-copilot.test.ts
+++ b/packages/coding-agent/test/discovery/github-copilot.test.ts
@@ -165,6 +165,24 @@ describe("github discovery — Copilot user-global surface", () => {
 		expect(resource.content.trim()).toBe("C# body");
 	});
 
+	test("splits comma-separated applyTo globs and treats **/* as always-apply (#2731)", async () => {
+		write(
+			path.join(cwd, ".github", "instructions", "ts.instructions.md"),
+			"---\napplyTo: '**/*.ts,**/*.tsx'\n---\nTS body\n",
+		);
+		write(path.join(cwd, ".github", "instructions", "all.instructions.md"), "---\napplyTo: '**/*'\n---\nAll body\n");
+
+		const result = await loadCapability<Rule>("rules", { cwd, providers: ["github"] });
+
+		const ts = result.items.find(rule => rule.name === "ts");
+		expect(ts?.alwaysApply).toBe(false);
+		expect(ts?.globs).toEqual(["**/*.ts", "**/*.tsx"]);
+
+		const all = result.items.find(rule => rule.name === "all");
+		expect(all?.alwaysApply).toBe(true);
+		expect(all?.globs).toBeUndefined();
+	});
+
 	test("disabled github provider suppresses copilot instructions and instruction-file rules (#2731)", async () => {
 		write(path.join(cwd, ".github", "copilot-instructions.md"), "project guidance");
 		write(