diff --git a/packages/coding-agent/src/discovery/claude.ts b/packages/coding-agent/src/discovery/claude.ts
index cd5bc71d8..69b5ca8b6 100644
--- a/packages/coding-agent/src/discovery/claude.ts
+++ b/packages/coding-agent/src/discovery/claude.ts
@@ -269,20 +269,27 @@ function readClaudeCommandToggles(): { enableUser: boolean; enableProject: boole
 	}
 }
 
-function getClaudeCommandNamespaceAlias(commandsDir: string, filePath: string): string | null {
-	const relativeName = path.relative(commandsDir, filePath).replace(/\.md$/, "");
-	if (!/[\\/]/.test(relativeName)) return null;
-	return relativeName.replace(/[\\/]+/g, ":");
+function getClaudeRelativeCommandName(commandsDir: string, filePath: string): string {
+	return path.relative(commandsDir, filePath).replace(/\.md$/, "");
 }
 
 function addClaudeCommandNamespaceAliases(commands: SlashCommand[], commandsDir: string): SlashCommand[] {
+	const rootCommands: SlashCommand[] = [];
+	const nestedCommands: SlashCommand[] = [];
 	const aliases: SlashCommand[] = [];
+
 	for (const command of commands) {
-		const alias = getClaudeCommandNamespaceAlias(commandsDir, command.path);
-		if (alias === null) continue;
-		aliases.push({ ...command, name: alias });
+		const relativeName = getClaudeRelativeCommandName(commandsDir, command.path);
+		if (!/[\\/]/.test(relativeName)) {
+			rootCommands.push(command);
+			continue;
+		}
+
+		nestedCommands.push(command);
+		aliases.push({ ...command, name: relativeName.replace(/[\\/]+/g, ":") });
 	}
-	return aliases.length === 0 ? commands : [...commands, ...aliases];
+
+	return nestedCommands.length === 0 ? commands : [...rootCommands, ...nestedCommands, ...aliases];
 }
 
 async function loadSlashCommands(ctx: LoadContext): Promise<LoadResult<SlashCommand>> {
diff --git a/packages/coding-agent/test/discovery/claude-commands.test.ts b/packages/coding-agent/test/discovery/claude-commands.test.ts
index 019d41b3e..77fc675ef 100644
--- a/packages/coding-agent/test/discovery/claude-commands.test.ts
+++ b/packages/coding-agent/test/discovery/claude-commands.test.ts
@@ -60,4 +60,23 @@ describe("Claude Code slash command discovery", () => {
 		expect(names).toContain("audit");
 		expect(names).toContain("team:audit");
 	});
+	test("keeps root commands ahead of nested basename duplicates", async () => {
+		const rootApply = path.join(project, ".claude", "commands", "apply.md");
+		const nestedApply = path.join(project, ".claude", "commands", "agent", "apply.md");
+		await writeFile(rootApply, "Root apply prompt\n");
+		await writeFile(nestedApply, "Nested apply prompt\n");
+
+		const result = await loadCapability<SlashCommand>(slashCommandCapability.id, {
+			cwd: project,
+			providers: ["claude"],
+		});
+		const apply = result.items.find(command => command.name === "apply");
+		const agentApply = result.items.find(command => command.name === "agent:apply");
+
+		expect(result.warnings).toEqual([]);
+		expect(apply?.path).toBe(rootApply);
+		expect(apply?.content).toBe("Root apply prompt\n");
+		expect(agentApply?.path).toBe(nestedApply);
+		expect(agentApply?.content).toBe("Nested apply prompt\n");
+	});
 });