fix(discovery): load file-form Claude plugin commands

Claude plugin manifests allow command path entries to name either directories
or flat `.md` command files. The array resolver was now preserving those file
paths, but `loadSlashCommands` still sent every resolved entry through
`loadFilesFromDir`, which only globs inside directories. A manifest such as
`{"commands":["./custom/deploy.md"]}` therefore replaced the default scan
and then loaded nothing.

Teach the command loader to stat each resolved entry: `.md` files are read as
single slash commands with the same plugin namespace and source metadata as
directory-loaded files; directories continue through `loadFilesFromDir`.
Missing entries keep the existing silent-empty behavior.

Add a regression test covering a mixed array of a direct command file and a
command directory while proving default `commands/` remains replaced unless
listed explicitly.

packages/coding-agent/src/discovery/claude-plugins.ts

@@ -4,6 +4,7 @@
  * Loads configuration from ~/.claude/plugins/cache/ based on installed_plugins.json registry.
  * Priority: 70 (below claude.ts at 80, so user overrides in .claude/ take precedence)
  */
+import * as fs from "node:fs/promises";
 import * as path from "node:path";
 import { logger } from "@oh-my-pi/pi-utils";
 import { registerProvider } from "../capability";
@@ -209,8 +210,31 @@ async function loadSlashCommands(ctx: LoadContext): Promise<LoadResult<SlashComm
 				false,
 			);
 			const commandResults = await Promise.all(
-				commandsDirs.map(dir =>
-					loadFilesFromDir<SlashCommand>(ctx, dir, PROVIDER_ID, root.scope, {
+				commandsDirs.map(async dir => {
+					try {
+						const stats = await fs.stat(dir);
+						if (stats.isFile()) {
+							if (path.extname(dir) !== ".md") return { items: [], warnings: [] };
+							const content = await readFile(dir);
+							if (content === null) return { items: [], warnings: [`Failed to read file: ${dir}`] };
+							const cmdName = path.basename(dir).replace(/\.md$/, "");
+							return {
+								items: [
+									{
+										name: root.plugin ? `${root.plugin}:${cmdName}` : cmdName,
+										path: dir,
+										content,
+										level: root.scope,
+										_source: createSourceMeta(PROVIDER_ID, dir, root.scope),
+									},
+								],
+								warnings: [],
+							};
+						}
+					} catch {
+						// Missing entries behave like missing directories: no items, no warning.
+					}
+					return loadFilesFromDir<SlashCommand>(ctx, dir, PROVIDER_ID, root.scope, {
 						extensions: ["md"],
 						transform: (name, content, filePath, source) => {
 							const cmdName = name.replace(/\.md$/, "");
@@ -222,8 +246,8 @@ async function loadSlashCommands(ctx: LoadContext): Promise<LoadResult<SlashComm
 								_source: source,
 							};
 						},
-					}),
-				),
+					});
+				}),
 			);
 			return { commandResults, resolveWarnings };
 		}),

packages/coding-agent/test/discovery/claude-plugins.test.ts

@@ -693,6 +693,48 @@ describe("listClaudePluginRoots", () => {
 		]);
 	});
 
+	test("reads slash commands from array-form manifest file entries", async () => {
+		// Claude plugins reference allows command paths to be either flat `.md`
+		// files or directories. A manifest-declared commands field still replaces
+		// default `commands/`; plugins that want defaults must list `./commands`.
+		const pluginsDir = path.join(tempDir, ".claude", "plugins");
+		const pluginPath = path.join(tempDir, "plugins", "manifest-commands-files");
+		await fs.mkdir(pluginsDir, { recursive: true });
+		await fs.mkdir(path.join(pluginPath, ".claude-plugin"), { recursive: true });
+		await fs.mkdir(path.join(pluginPath, "custom"), { recursive: true });
+		await fs.mkdir(path.join(pluginPath, "ops"), { recursive: true });
+		await fs.mkdir(path.join(pluginPath, "commands"), { recursive: true });
+
+		const registry = {
+			version: 2,
+			plugins: {
+				"manifest-commands-files@market": [
+					{
+						scope: "user",
+						installPath: pluginPath,
+						version: "1.0.0",
+						installedAt: "2025-01-01T00:00:00Z",
+						lastUpdated: "2025-01-01T00:00:00Z",
+					},
+				],
+			},
+		};
+		await fs.writeFile(path.join(pluginsDir, "installed_plugins.json"), JSON.stringify(registry));
+		await fs.writeFile(
+			path.join(pluginPath, ".claude-plugin", "plugin.json"),
+			JSON.stringify({ commands: ["./custom/deploy.md", "./ops"] }),
+		);
+		await fs.writeFile(path.join(pluginPath, "custom", "deploy.md"), "Deploy\n");
+		await fs.writeFile(path.join(pluginPath, "ops", "rollback.md"), "Rollback\n");
+		await fs.writeFile(path.join(pluginPath, "commands", "default.md"), "Default\n");
+
+		const result = await loadCapability<SlashCommand>("slash-commands", { cwd: tempDir });
+		expect(result.warnings).toEqual([]);
+		expect(result.all.find(c => c.name === "manifest-commands-files:deploy")?.content).toBe("Deploy\n");
+		expect(result.all.find(c => c.name === "manifest-commands-files:rollback")?.content).toBe("Rollback\n");
+		expect(result.all.find(c => c.name === "manifest-commands-files:default")).toBeUndefined();
+	});
+
 	test("array-form commands warns on out-of-root entries while loading valid ones", async () => {
 		const pluginsDir = path.join(tempDir, ".claude", "plugins");
 		const pluginPath = path.join(tempDir, "plugins", "manifest-commands-mixed");