revert(pi): reset carried vendored source deltas

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

@@ -459,14 +459,14 @@ function findGitRepoRoot(startDir: string): string | null {
 	}
 }
 
-function collectAncestorConfigDirs(startDir: string, configDirName: string): string[] {
-	const configDirs: string[] = [];
+function collectAncestorAgentsSkillDirs(startDir: string): string[] {
+	const skillDirs: string[] = [];
 	const resolvedStartDir = resolve(startDir);
 	const gitRepoRoot = findGitRepoRoot(resolvedStartDir);
 
 	let dir = resolvedStartDir;
 	while (true) {
-		configDirs.push(join(dir, configDirName));
+		skillDirs.push(join(dir, ".agents", "skills"));
 		if (gitRepoRoot && dir === gitRepoRoot) {
 			break;
 		}
@@ -477,7 +477,7 @@ function collectAncestorConfigDirs(startDir: string, configDirName: string): str
 		dir = parent;
 	}
 
-	return configDirs;
+	return skillDirs;
 }
 
 function collectAutoPromptEntries(dir: string): string[] {
@@ -2388,13 +2388,16 @@ export class DefaultPackageManager implements PackageManager {
 			prompts: join(globalBaseDir, "prompts"),
 			themes: join(globalBaseDir, "themes"),
 		};
+		const projectDirs = {
+			extensions: join(projectBaseDir, "extensions"),
+			skills: join(projectBaseDir, "skills"),
+			prompts: join(projectBaseDir, "prompts"),
+			themes: join(projectBaseDir, "themes"),
+		};
 		const userAgentsSkillsDir = join(getHomeDir(), ".agents", "skills");
 		const projectTrusted = this.settingsManager.isProjectTrusted();
-		const projectConfigDirs = projectTrusted
-			? collectAncestorConfigDirs(this.cwd, CONFIG_DIR_NAME).filter((dir) => resolve(dir) !== resolve(globalBaseDir))
-			: [];
-		const projectAgentsDirs = projectTrusted
-			? collectAncestorConfigDirs(this.cwd, ".agents").filter((dir) => resolve(dir) !== resolve(dirname(userAgentsSkillsDir)))
+		const projectAgentsSkillDirs = projectTrusted
+			? collectAncestorAgentsSkillDirs(this.cwd).filter((dir) => resolve(dir) !== resolve(userAgentsSkillsDir))
 			: [];
 
 		const addResources = (
@@ -2411,54 +2414,56 @@ export class DefaultPackageManager implements PackageManager {
 			}
 		};
 
-		// Project resources from .pi/ in cwd and ancestors.
-		for (const configDir of projectConfigDirs) {
-			const configMetadata: PathMetadata = {
-				...projectMetadata,
-				baseDir: configDir,
-			};
+		if (projectTrusted) {
+			// Project extensions from .pi/
 			addResources(
 				"extensions",
-				collectAutoExtensionEntries(join(configDir, "extensions")),
-				configMetadata,
+				collectAutoExtensionEntries(projectDirs.extensions),
+				projectMetadata,
 				projectOverrides.extensions,
-				configDir,
+				projectBaseDir,
 			);
+
+			// Project skills from .pi/
 			addResources(
 				"skills",
-				collectAutoSkillEntries(join(configDir, "skills"), "pi"),
-				configMetadata,
+				collectAutoSkillEntries(projectDirs.skills, "pi"),
+				projectMetadata,
 				projectOverrides.skills,
-				configDir,
-			);
-			addResources(
-				"prompts",
-				collectAutoPromptEntries(join(configDir, "prompts")),
-				configMetadata,
-				projectOverrides.prompts,
-				configDir,
-			);
-			addResources(
-				"themes",
-				collectAutoThemeEntries(join(configDir, "themes")),
-				configMetadata,
-				projectOverrides.themes,
-				configDir,
+				projectBaseDir,
 			);
 		}
 
-		// Project skills from .agents/ in cwd and ancestors.
-		for (const agentsDir of projectAgentsDirs) {
+		// 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: agentsDir,
+				baseDir: agentsBaseDir,
 			};
 			addResources(
 				"skills",
-				collectAutoSkillEntries(join(agentsDir, "skills"), "agents"),
+				collectAutoSkillEntries(agentsSkillsDir, "agents"),
 				agentsMetadata,
 				projectOverrides.skills,
-				agentsDir,
+				agentsBaseDir,
+			);
+		}
+
+		if (projectTrusted) {
+			addResources(
+				"prompts",
+				collectAutoPromptEntries(projectDirs.prompts),
+				projectMetadata,
+				projectOverrides.prompts,
+				projectBaseDir,
+			);
+			addResources(
+				"themes",
+				collectAutoThemeEntries(projectDirs.themes),
+				projectMetadata,
+				projectOverrides.themes,
+				projectBaseDir,
 			);
 		}
 

third_party/pi/packages/coding-agent/src/utils/tools-manager.ts

@@ -72,8 +72,8 @@ const TOOLS: Record<string, ToolConfig> = {
 function commandExists(cmd: string): boolean {
 	try {
 		const result = spawnSync(cmd, ["--version"], { stdio: "pipe" });
-		// Downloaded generic Linux binaries can exist but fail on NixOS before they print a version.
-		return (result.error === undefined || result.error === null) && result.status === 0;
+		// Check for ENOENT error (command not found)
+		return result.error === undefined || result.error === null;
 	} catch {
 		return false;
 	}
@@ -86,7 +86,7 @@ export function getToolPath(tool: "fd" | "rg"): string | null {
 
 	// Check our tools directory first
 	const localPath = join(TOOLS_DIR, config.binaryName + (platform() === "win32" ? ".exe" : ""));
-	if (existsSync(localPath) && commandExists(localPath)) {
+	if (existsSync(localPath)) {
 		return localPath;
 	}