fix(coding-agent): align auto-discovery with loader rules

packages/coding-agent/src/core/package-manager.ts

@@ -169,7 +169,7 @@ function collectFiles(dir: string, filePattern: RegExp, skipNodeModules = true):
 	return files;
 }
 
-function collectSkillEntries(dir: string): string[] {
+function collectSkillEntries(dir: string, includeRootFiles = true): string[] {
 	const entries: string[] = [];
 	if (!existsSync(dir)) return entries;
 
@@ -194,14 +194,13 @@ function collectSkillEntries(dir: string): string[] {
 			}
 
 			if (isDir) {
-				const skillMd = join(fullPath, "SKILL.md");
-				if (existsSync(skillMd)) {
+				entries.push(...collectSkillEntries(fullPath, false));
+			} else if (isFile) {
+				const isRootMd = includeRootFiles && entry.name.endsWith(".md");
+				const isSkillMd = !includeRootFiles && entry.name === "SKILL.md";
+				if (isRootMd || isSkillMd) {
 					entries.push(fullPath);
-				} else {
-					entries.push(...collectSkillEntries(fullPath));
 				}
-			} else if (isFile && entry.name.endsWith(".md")) {
-				entries.push(fullPath);
 			}
 		}
 	} catch {
@@ -211,48 +210,8 @@ function collectSkillEntries(dir: string): string[] {
 	return entries;
 }
 
-function collectAutoSkillEntries(dir: string, isRoot = true): string[] {
-	const entries: string[] = [];
-	if (!existsSync(dir)) return entries;
-
-	try {
-		const dirEntries = readdirSync(dir, { withFileTypes: true });
-		for (const entry of dirEntries) {
-			if (entry.name.startsWith(".")) continue;
-			if (entry.name === "node_modules") continue;
-
-			const fullPath = join(dir, entry.name);
-			let isDir = entry.isDirectory();
-			let isFile = entry.isFile();
-
-			if (entry.isSymbolicLink()) {
-				try {
-					const stats = statSync(fullPath);
-					isDir = stats.isDirectory();
-					isFile = stats.isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			if (isDir) {
-				const skillMd = join(fullPath, "SKILL.md");
-				if (existsSync(skillMd)) {
-					entries.push(fullPath);
-				} else {
-					entries.push(...collectAutoSkillEntries(fullPath, false));
-				}
-			} else if (isFile && entry.name.endsWith(".md")) {
-				if (isRoot || entry.name === "SKILL.md") {
-					entries.push(fullPath);
-				}
-			}
-		}
-	} catch {
-		// Ignore errors
-	}
-
-	return entries;
+function collectAutoSkillEntries(dir: string, includeRootFiles = true): string[] {
+	return collectSkillEntries(dir, includeRootFiles);
 }
 
 function collectAutoPromptEntries(dir: string): string[] {
@@ -400,9 +359,18 @@ function collectAutoExtensionEntries(dir: string): string[] {
 function matchesAnyPattern(filePath: string, patterns: string[], baseDir: string): boolean {
 	const rel = relative(baseDir, filePath);
 	const name = basename(filePath);
-	return patterns.some(
-		(pattern) => minimatch(rel, pattern) || minimatch(name, pattern) || minimatch(filePath, pattern),
-	);
+	const isSkillFile = name === "SKILL.md";
+	const parentDir = isSkillFile ? dirname(filePath) : undefined;
+	const parentRel = isSkillFile ? relative(baseDir, parentDir!) : undefined;
+	const parentName = isSkillFile ? basename(parentDir!) : undefined;
+
+	return patterns.some((pattern) => {
+		if (minimatch(rel, pattern) || minimatch(name, pattern) || minimatch(filePath, pattern)) {
+			return true;
+		}
+		if (!isSkillFile) return false;
+		return minimatch(parentRel!, pattern) || minimatch(parentName!, pattern) || minimatch(parentDir!, pattern);
+	});
 }
 
 function normalizeExactPattern(pattern: string): string {
@@ -415,9 +383,18 @@ function normalizeExactPattern(pattern: string): string {
 function matchesAnyExactPattern(filePath: string, patterns: string[], baseDir: string): boolean {
 	if (patterns.length === 0) return false;
 	const rel = relative(baseDir, filePath);
+	const name = basename(filePath);
+	const isSkillFile = name === "SKILL.md";
+	const parentDir = isSkillFile ? dirname(filePath) : undefined;
+	const parentRel = isSkillFile ? relative(baseDir, parentDir!) : undefined;
+
 	return patterns.some((pattern) => {
 		const normalized = normalizeExactPattern(pattern);
-		return normalized === rel || normalized === filePath;
+		if (normalized === rel || normalized === filePath) {
+			return true;
+		}
+		if (!isSkillFile) return false;
+		return normalized === parentRel || normalized === parentDir;
 	});
 }
 

packages/coding-agent/src/core/resource-loader.ts

@@ -268,24 +268,52 @@ export class DefaultResourceLoader implements ResourceLoader {
 		});
 
 		// Helper to extract enabled paths and store metadata
-		const getEnabledPaths = (
+		const getEnabledResources = (
 			resources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,
-		): string[] => {
+		): Array<{ path: string; enabled: boolean; metadata: PathMetadata }> => {
 			for (const r of resources) {
 				if (!this.pathMetadata.has(r.path)) {
 					this.pathMetadata.set(r.path, r.metadata);
 				}
 			}
-			return resources.filter((r) => r.enabled).map((r) => r.path);
+			return resources.filter((r) => r.enabled);
 		};
 
+		const getEnabledPaths = (
+			resources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,
+		): string[] => getEnabledResources(resources).map((r) => r.path);
+
 		// Store metadata and get enabled paths
 		this.pathMetadata = new Map();
 		const enabledExtensions = getEnabledPaths(resolvedPaths.extensions);
-		const enabledSkills = getEnabledPaths(resolvedPaths.skills);
+		const enabledSkillResources = getEnabledResources(resolvedPaths.skills);
 		const enabledPrompts = getEnabledPaths(resolvedPaths.prompts);
 		const enabledThemes = getEnabledPaths(resolvedPaths.themes);
 
+		const mapSkillPath = (resource: { path: string; metadata: PathMetadata }): string => {
+			if (resource.metadata.source !== "auto" && resource.metadata.origin !== "package") {
+				return resource.path;
+			}
+			try {
+				const stats = statSync(resource.path);
+				if (!stats.isDirectory()) {
+					return resource.path;
+				}
+			} catch {
+				return resource.path;
+			}
+			const skillFile = join(resource.path, "SKILL.md");
+			if (existsSync(skillFile)) {
+				if (!this.pathMetadata.has(skillFile)) {
+					this.pathMetadata.set(skillFile, resource.metadata);
+				}
+				return skillFile;
+			}
+			return resource.path;
+		};
+
+		const enabledSkills = enabledSkillResources.map(mapSkillPath);
+
 		// Add CLI paths metadata
 		for (const r of cliExtensionPaths.extensions) {
 			if (!this.pathMetadata.has(r.path)) {

packages/coding-agent/src/modes/interactive/components/config-selector.ts

@@ -98,12 +98,14 @@ function buildGroups(resolved: ResolvedPaths): ResourceGroup[] {
 				group.subgroups.push(subgroup);
 			}
 
+			const displayName =
+				resourceType === "skills" && basename(path) === "SKILL.md" ? basename(dirname(path)) : basename(path);
 			subgroup.items.push({
 				path,
 				enabled,
 				metadata,
 				resourceType,
-				displayName: basename(path),
+				displayName,
 				groupKey,
 				subgroupKey,
 			});

packages/coding-agent/test/package-manager.test.ts

@@ -59,8 +59,9 @@ describe("DefaultPackageManager", () => {
 		it("should resolve skill paths from settings", async () => {
 			const skillDir = join(agentDir, "skills", "my-skill");
 			mkdirSync(skillDir, { recursive: true });
+			const skillFile = join(skillDir, "SKILL.md");
 			writeFileSync(
-				join(skillDir, "SKILL.md"),
+				skillFile,
 				`---
 name: test-skill
 description: A test skill
@@ -71,8 +72,8 @@ Content`,
 			settingsManager.setSkillPaths(["skills"]);
 
 			const result = await packageManager.resolve();
-			// Skills with SKILL.md are returned as directory paths
-			expect(result.skills.some((r) => r.path === skillDir && r.enabled)).toBe(true);
+			// Skills with SKILL.md are returned as file paths
+			expect(result.skills.some((r) => r.path === skillFile && r.enabled)).toBe(true);
 		});
 
 		it("should resolve project paths relative to .pi", async () => {
@@ -144,8 +145,10 @@ Content`,
 
 			const result = await packageManager.resolveExtensionSources([pkgDir]);
 			expect(result.extensions.some((r) => r.path === join(pkgDir, "src", "index.ts") && r.enabled)).toBe(true);
-			// Skills with SKILL.md are returned as directory paths
-			expect(result.skills.some((r) => r.path === join(pkgDir, "skills", "my-skill") && r.enabled)).toBe(true);
+			// Skills with SKILL.md are returned as file paths
+			expect(result.skills.some((r) => r.path === join(pkgDir, "skills", "my-skill", "SKILL.md") && r.enabled)).toBe(
+				true,
+			);
 		});
 
 		it("should handle directories with auto-discovery layout", async () => {

packages/coding-agent/test/resource-loader.test.ts

@@ -3,6 +3,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import { DefaultResourceLoader } from "../src/core/resource-loader.js";
+import { SettingsManager } from "../src/core/settings-manager.js";
 import type { Skill } from "../src/core/skills.js";
 
 describe("DefaultResourceLoader", () => {
@@ -51,6 +52,27 @@ Skill content here.`,
 			expect(skills.some((s) => s.name === "test-skill")).toBe(true);
 		});
 
+		it("should ignore extra markdown files in auto-discovered skill dirs", async () => {
+			const skillDir = join(agentDir, "skills", "pi-skills", "browser-tools");
+			mkdirSync(skillDir, { recursive: true });
+			writeFileSync(
+				join(skillDir, "SKILL.md"),
+				`---
+name: browser-tools
+description: Browser tools
+---
+Skill content here.`,
+			);
+			writeFileSync(join(skillDir, "EFFICIENCY.md"), "No frontmatter here");
+
+			const loader = new DefaultResourceLoader({ cwd, agentDir });
+			await loader.reload();
+
+			const { skills, diagnostics } = loader.getSkills();
+			expect(skills.some((s) => s.name === "browser-tools")).toBe(true);
+			expect(diagnostics.some((d) => d.path?.endsWith("EFFICIENCY.md"))).toBe(false);
+		});
+
 		it("should discover prompts from agentDir", async () => {
 			const promptsDir = join(agentDir, "prompts");
 			mkdirSync(promptsDir, { recursive: true });
@@ -69,6 +91,50 @@ Prompt content.`,
 			expect(prompts.some((p) => p.name === "test-prompt")).toBe(true);
 		});
 
+		it("should honor overrides for auto-discovered resources", async () => {
+			const settingsManager = SettingsManager.inMemory();
+			settingsManager.setExtensionPaths(["-extensions/disabled.ts"]);
+			settingsManager.setSkillPaths(["-skills/skip-skill"]);
+			settingsManager.setPromptTemplatePaths(["-prompts/skip.md"]);
+			settingsManager.setThemePaths(["-themes/skip.json"]);
+
+			const extensionsDir = join(agentDir, "extensions");
+			mkdirSync(extensionsDir, { recursive: true });
+			writeFileSync(join(extensionsDir, "disabled.ts"), "export default function() {}");
+
+			const skillDir = join(agentDir, "skills", "skip-skill");
+			mkdirSync(skillDir, { recursive: true });
+			writeFileSync(
+				join(skillDir, "SKILL.md"),
+				`---
+name: skip-skill
+description: Skip me
+---
+Content`,
+			);
+
+			const promptsDir = join(agentDir, "prompts");
+			mkdirSync(promptsDir, { recursive: true });
+			writeFileSync(join(promptsDir, "skip.md"), "Skip prompt");
+
+			const themesDir = join(agentDir, "themes");
+			mkdirSync(themesDir, { recursive: true });
+			writeFileSync(join(themesDir, "skip.json"), "{}");
+
+			const loader = new DefaultResourceLoader({ cwd, agentDir, settingsManager });
+			await loader.reload();
+
+			const { extensions } = loader.getExtensions();
+			const { skills } = loader.getSkills();
+			const { prompts } = loader.getPrompts();
+			const { themes } = loader.getThemes();
+
+			expect(extensions.some((e) => e.path.endsWith("disabled.ts"))).toBe(false);
+			expect(skills.some((s) => s.name === "skip-skill")).toBe(false);
+			expect(prompts.some((p) => p.name === "skip")).toBe(false);
+			expect(themes.some((t) => t.sourcePath?.endsWith("skip.json"))).toBe(false);
+		});
+
 		it("should discover AGENTS.md context files", async () => {
 			writeFileSync(join(cwd, "AGENTS.md"), "# Project Guidelines\n\nBe helpful.");