Merge pull request #4299 from aliou/fix/resource-location-in-config-tui

fix(coding-agent): preserve .agents provenance in skill metadata

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

@@ -2182,6 +2182,7 @@ export class DefaultPackageManager implements PackageManager {
 			}
 		};
 
+		// Project extensions from .pi/
 		addResources(
 			"extensions",
 			collectAutoExtensionEntries(projectDirs.extensions),
@@ -2189,16 +2190,32 @@ export class DefaultPackageManager implements PackageManager {
 			projectOverrides.extensions,
 			projectBaseDir,
 		);
+
+		// Project skills from .pi/
 		addResources(
 			"skills",
-			[
+			collectAutoSkillEntries(projectDirs.skills, "pi"),
-				...collectAutoSkillEntries(projectDirs.skills, "pi"),
-				...projectAgentsSkillDirs.flatMap((dir) => collectAutoSkillEntries(dir, "agents")),
-			],
 			projectMetadata,
 			projectOverrides.skills,
 			projectBaseDir,
 		);
+
+		// Project skills from .agents/ (each with its own baseDir)
+		for (const agentsSkillsDir of projectAgentsSkillDirs) {
+			const agentsBaseDir = dirname(agentsSkillsDir); // the .agents directory
+			const agentsMetadata: PathMetadata = {
+				...projectMetadata,
+				baseDir: agentsBaseDir,
+			};
+			addResources(
+				"skills",
+				collectAutoSkillEntries(agentsSkillsDir, "agents"),
+				agentsMetadata,
+				projectOverrides.skills,
+				agentsBaseDir,
+			);
+		}
+
 		addResources(
 			"prompts",
 			collectAutoPromptEntries(projectDirs.prompts),
@@ -2214,6 +2231,7 @@ export class DefaultPackageManager implements PackageManager {
 			projectBaseDir,
 		);
 
+		// User extensions from ~/.pi/agent/
 		addResources(
 			"extensions",
 			collectAutoExtensionEntries(userDirs.extensions),
@@ -2221,13 +2239,30 @@ export class DefaultPackageManager implements PackageManager {
 			userOverrides.extensions,
 			globalBaseDir,
 		);
+
+		// User skills from ~/.pi/agent/
 		addResources(
 			"skills",
-			[...collectAutoSkillEntries(userDirs.skills, "pi"), ...collectAutoSkillEntries(userAgentsSkillsDir, "agents")],
+			collectAutoSkillEntries(userDirs.skills, "pi"),
 			userMetadata,
 			userOverrides.skills,
 			globalBaseDir,
 		);
+
+		// User skills from ~/.agents/ (with its own baseDir)
+		const userAgentsBaseDir = dirname(userAgentsSkillsDir);
+		const userAgentsMetadata: PathMetadata = {
+			...userMetadata,
+			baseDir: userAgentsBaseDir,
+		};
+		addResources(
+			"skills",
+			collectAutoSkillEntries(userAgentsSkillsDir, "agents"),
+			userAgentsMetadata,
+			userOverrides.skills,
+			userAgentsBaseDir,
+		);
+
 		addResources(
 			"prompts",
 			collectAutoPromptEntries(userDirs.prompts),

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

@@ -2,6 +2,7 @@
  * TUI component for managing package resources (enable/disable)
  */
 
+import { homedir } from "node:os";
 import { basename, dirname, join, relative } from "node:path";
 import {
 	type Component,
@@ -55,12 +56,34 @@ interface ResourceGroup {
 	subgroups: ResourceSubgroup[];
 }
 
+function formatBaseDir(baseDir: string): string {
+	const homeDir = homedir();
+	let displayPath: string;
+
+	if (baseDir === homeDir) {
+		displayPath = "~";
+	} else if (baseDir.startsWith(homeDir)) {
+		// Replace home prefix with ~, normalize separators for display
+		const rest = baseDir.slice(homeDir.length);
+		displayPath = `~${rest.replace(/\\/g, "/")}`;
+	} else {
+		displayPath = baseDir.replace(/\\/g, "/");
+	}
+
+	return displayPath.endsWith("/") ? displayPath : `${displayPath}/`;
+}
+
 function getGroupLabel(metadata: PathMetadata): string {
 	if (metadata.origin === "package") {
 		return `${metadata.source} (${metadata.scope})`;
 	}
 	// Top-level resources
 	if (metadata.source === "auto") {
+		if (metadata.baseDir) {
+			return metadata.scope === "user"
+				? `User (${formatBaseDir(metadata.baseDir)})`
+				: `Project (${formatBaseDir(metadata.baseDir)})`;
+		}
 		return metadata.scope === "user" ? "User (~/.pi/agent/)" : "Project (.pi/)";
 	}
 	return metadata.scope === "user" ? "User settings" : "Project settings";
@@ -72,7 +95,7 @@ function buildGroups(resolved: ResolvedPaths): ResourceGroup[] {
 	const addToGroup = (resources: ResolvedResource[], resourceType: ResourceType) => {
 		for (const res of resources) {
 			const { path, enabled, metadata } = res;
-			const groupKey = `${metadata.origin}:${metadata.scope}:${metadata.source}`;
+			const groupKey = `${metadata.origin}:${metadata.scope}:${metadata.source}:${metadata.baseDir ?? ""}`;
 
 			if (!groupMap.has(groupKey)) {
 				groupMap.set(groupKey, {

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

@@ -274,6 +274,94 @@ Content`,
 		});
 	});
 
+	describe("auto-discovered skill metadata", () => {
+		it("should use the agent dir as baseDir for user .pi/agent skills", async () => {
+			const skillPath = join(agentDir, "skills", "user-pi", "SKILL.md");
+			mkdirSync(join(agentDir, "skills", "user-pi"), { recursive: true });
+			writeFileSync(skillPath, "---\nname: user-pi\ndescription: user pi\n---\n");
+
+			const result = await packageManager.resolve();
+			const skill = result.skills.find((r) => r.path === skillPath);
+
+			expect(skill?.metadata.source).toBe("auto");
+			expect(skill?.metadata.scope).toBe("user");
+			expect(skill?.metadata.baseDir).toBe(agentDir);
+		});
+
+		it("should use the project .pi dir as baseDir for project .pi skills", async () => {
+			const projectBaseDir = join(tempDir, ".pi");
+			const skillPath = join(projectBaseDir, "skills", "project-pi", "SKILL.md");
+			mkdirSync(join(projectBaseDir, "skills", "project-pi"), { recursive: true });
+			writeFileSync(skillPath, "---\nname: project-pi\ndescription: project pi\n---\n");
+
+			const result = await packageManager.resolve();
+			const skill = result.skills.find((r) => r.path === skillPath);
+
+			expect(skill?.metadata.source).toBe("auto");
+			expect(skill?.metadata.scope).toBe("project");
+			expect(skill?.metadata.baseDir).toBe(projectBaseDir);
+		});
+
+		it("should use ~/.agents as baseDir for user .agents skills", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const agentsBaseDir = join(tempDir, ".agents");
+				const skillPath = join(agentsBaseDir, "skills", "user-agents", "SKILL.md");
+				mkdirSync(join(agentsBaseDir, "skills", "user-agents"), { recursive: true });
+				writeFileSync(skillPath, "---\nname: user-agents\ndescription: user agents\n---\n");
+
+				const result = await packageManager.resolve();
+				const skill = result.skills.find((r) => r.path === skillPath);
+
+				expect(skill?.metadata.source).toBe("auto");
+				expect(skill?.metadata.scope).toBe("user");
+				expect(skill?.metadata.baseDir).toBe(agentsBaseDir);
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
+
+		it("should use each project .agents dir as baseDir for project .agents skills", async () => {
+			const repoRoot = join(tempDir, "repo");
+			const nestedCwd = join(repoRoot, "packages", "feature");
+			mkdirSync(nestedCwd, { recursive: true });
+			mkdirSync(join(repoRoot, ".git"), { recursive: true });
+
+			const repoAgentsBaseDir = join(repoRoot, ".agents");
+			const repoSkill = join(repoAgentsBaseDir, "skills", "repo", "SKILL.md");
+			mkdirSync(join(repoAgentsBaseDir, "skills", "repo"), { recursive: true });
+			writeFileSync(repoSkill, "---\nname: repo\ndescription: repo\n---\n");
+
+			const packageAgentsBaseDir = join(repoRoot, "packages", ".agents");
+			const packageSkill = join(packageAgentsBaseDir, "skills", "package", "SKILL.md");
+			mkdirSync(join(packageAgentsBaseDir, "skills", "package"), { recursive: true });
+			writeFileSync(packageSkill, "---\nname: package\ndescription: package\n---\n");
+
+			const pm = new DefaultPackageManager({
+				cwd: nestedCwd,
+				agentDir,
+				settingsManager,
+			});
+
+			const result = await pm.resolve();
+			const resolvedRepoSkill = result.skills.find((r) => r.path === repoSkill);
+			const resolvedPackageSkill = result.skills.find((r) => r.path === packageSkill);
+
+			expect(resolvedRepoSkill?.metadata.source).toBe("auto");
+			expect(resolvedRepoSkill?.metadata.scope).toBe("project");
+			expect(resolvedRepoSkill?.metadata.baseDir).toBe(repoAgentsBaseDir);
+			expect(resolvedPackageSkill?.metadata.source).toBe("auto");
+			expect(resolvedPackageSkill?.metadata.scope).toBe("project");
+			expect(resolvedPackageSkill?.metadata.baseDir).toBe(packageAgentsBaseDir);
+		});
+	});
+
 	describe(".agents/skills auto-discovery", () => {
 		it("should scan .agents/skills from cwd up to git repo root", async () => {
 			const repoRoot = join(tempDir, "repo");