docs(agents): clarify Pi package source

AGENTS.md

@@ -118,6 +118,7 @@
 - OMP does not discover project skills from `.pi/skills`.
   Put skills shared by Pi and OMP under `.agents/skills`, or configure OMP's `skills.customDirectories`.
 - Pi is vendored under `third_party/pi` as a linear vendor import.
+  `pkgs.alexion.pi-coding-agent` packages that source and does not use Nixpkgs Pi.
   Do not use `git subtree add` or `git subtree pull` for Pi PR branches.
   Gitea rebases the synthetic upstream root commit without the `third_party/pi` prefix.
   Preserve `git-subtree-dir` and `git-subtree-split` trailers on Pi vendor commits.

src/flake/packages/pi-coding-agent.nix

@@ -1,8 +1,4 @@
-{
-  pi-coding-agent,
-  root,
-}:
-pi-coding-agent.overrideAttrs {
-  src = root + "/third_party/pi";
-  patches = [ ];
+{ pkgs, root }:
+pkgs.callPackage (root + "/third_party/pi/nix/package.nix") {
+  source = root + "/third_party/pi";
 }

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

@@ -471,14 +471,14 @@ function findGitRepoRoot(startDir: string): string | null {
 	}
 }
 
-function collectAncestorAgentsSkillDirs(startDir: string): string[] {
-	const skillDirs: string[] = [];
+function collectAncestorConfigDirs(startDir: string, configDirName: string): string[] {
+	const configDirs: string[] = [];
 	const resolvedStartDir = resolve(startDir);
 	const gitRepoRoot = findGitRepoRoot(resolvedStartDir);
 
 	let dir = resolvedStartDir;
 	while (true) {
-		skillDirs.push(join(dir, ".agents", "skills"));
+		configDirs.push(join(dir, configDirName));
 		if (gitRepoRoot && dir === gitRepoRoot) {
 			break;
 		}
@@ -489,7 +489,7 @@ function collectAncestorAgentsSkillDirs(startDir: string): string[] {
 		dir = parent;
 	}
 
-	return skillDirs;
+	return configDirs;
 }
 
 function collectAutoPromptEntries(dir: string): string[] {
@@ -2455,16 +2455,13 @@ 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 projectAgentsSkillDirs = projectTrusted
-			? collectAncestorAgentsSkillDirs(this.cwd).filter((dir) => resolve(dir) !== resolve(userAgentsSkillsDir))
+		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 addResources = (
@@ -2481,56 +2478,54 @@ export class DefaultPackageManager implements PackageManager {
 			}
 		};
 
-		if (projectTrusted) {
-			// Project extensions from .pi/
-			addResources(
-				"extensions",
-				collectAutoExtensionEntries(projectDirs.extensions),
-				projectMetadata,
-				projectOverrides.extensions,
-				projectBaseDir,
-			);
-
-			// Project skills from .pi/
-			addResources(
-				"skills",
-				collectAutoSkillEntries(projectDirs.skills, "pi"),
-				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 = {
+		// Project resources from .pi/ in cwd and ancestors.
+		for (const configDir of projectConfigDirs) {
+			const configMetadata: PathMetadata = {
 				...projectMetadata,
-				baseDir: agentsBaseDir,
+				baseDir: configDir,
 			};
 			addResources(
-				"skills",
-				collectAutoSkillEntries(agentsSkillsDir, "agents"),
-				agentsMetadata,
-				projectOverrides.skills,
-				agentsBaseDir,
+				"extensions",
+				collectAutoExtensionEntries(join(configDir, "extensions")),
+				configMetadata,
+				projectOverrides.extensions,
+				configDir,
+			);
+			addResources(
+				"skills",
+				collectAutoSkillEntries(join(configDir, "skills"), "pi"),
+				configMetadata,
+				projectOverrides.skills,
+				configDir,
 			);
-		}
-
-		if (projectTrusted) {
 			addResources(
 				"prompts",
-				collectAutoPromptEntries(projectDirs.prompts),
-				projectMetadata,
+				collectAutoPromptEntries(join(configDir, "prompts")),
+				configMetadata,
 				projectOverrides.prompts,
-				projectBaseDir,
+				configDir,
 			);
 			addResources(
 				"themes",
-				collectAutoThemeEntries(projectDirs.themes),
-				projectMetadata,
+				collectAutoThemeEntries(join(configDir, "themes")),
+				configMetadata,
 				projectOverrides.themes,
-				projectBaseDir,
+				configDir,
+			);
+		}
+
+		// Project skills from .agents/ in cwd and ancestors.
+		for (const agentsDir of projectAgentsDirs) {
+			const agentsMetadata: PathMetadata = {
+				...projectMetadata,
+				baseDir: agentsDir,
+			};
+			addResources(
+				"skills",
+				collectAutoSkillEntries(join(agentsDir, "skills"), "agents"),
+				agentsMetadata,
+				projectOverrides.skills,
+				agentsDir,
 			);
 		}