fix(coding-agent): avoid duplicate symlinked skills in pi config (#3417)

- dedupe resolved skill entries by canonical path (realpathSync) with raw-path fallback matching loadSkills()

- preserve precedence by applying skill dedupe after resource precedence sorting (first winner retained)

- add tests to verify expected behavior

- closes #3405

packages/coding-agent/CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+### Fixed
+
+- Fixed skill resolution to dedupe symlinked aliases by canonical path, so `pi config` no longer shows duplicate skill entries when `~/.pi/agent/skills` points to `~/.agents/skills` ([#3405](https://github.com/badlogic/pi-mono/issues/3405))
+
 ## [0.67.68] - 2026-04-17
 
 ## [0.67.67] - 2026-04-17

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

@@ -1,6 +1,15 @@
 import { type ChildProcess, type ChildProcessByStdio, spawn, spawnSync } from "node:child_process";
 import { createHash } from "node:crypto";
-import { existsSync, mkdirSync, readdirSync, readFileSync, rmSync, statSync, writeFileSync } from "node:fs";
+import {
+	existsSync,
+	mkdirSync,
+	readdirSync,
+	readFileSync,
+	realpathSync,
+	rmSync,
+	statSync,
+	writeFileSync,
+} from "node:fs";
 import { homedir, tmpdir } from "node:os";
 import { basename, dirname, join, relative, resolve, sep } from "node:path";
 import type { Readable } from "node:stream";
@@ -2190,9 +2199,28 @@ export class DefaultPackageManager implements PackageManager {
 			return resolved;
 		};
 
+		const seenCanonicalSkillPaths = new Set<string>();
+		const resolvedSkills = toResolved(accumulator.skills).filter((entry) => {
+			let canonicalPath: string;
+			try {
+				// Resolve symlink aliases to detect duplicate files.
+				canonicalPath = realpathSync(entry.path);
+			} catch {
+				// Fallback to raw path to match loadSkills() behavior.
+				canonicalPath = entry.path;
+			}
+
+			if (seenCanonicalSkillPaths.has(canonicalPath)) {
+				return false;
+			}
+
+			seenCanonicalSkillPaths.add(canonicalPath);
+			return true;
+		});
+
 		return {
 			extensions: toResolved(accumulator.extensions),
-			skills: toResolved(accumulator.skills),
+			skills: resolvedSkills,
 			prompts: toResolved(accumulator.prompts),
 			themes: toResolved(accumulator.themes),
 		};

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

@@ -1,5 +1,5 @@
 import { EventEmitter } from "node:events";
-import { mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { mkdirSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join, relative } from "node:path";
 import { PassThrough } from "node:stream";
@@ -315,6 +315,35 @@ Content`,
 				}
 			}
 		});
+
+		it("should dedupe user skill entries when ~/.pi/agent/skills is a symlink to ~/.agents/skills", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const agentSkillsDir = join(agentDir, "skills");
+				const agentsSkillsDir = join(tempDir, ".agents", "skills");
+				mkdirSync(agentsSkillsDir, { recursive: true });
+				// Use junction on Windows to avoid EPERM when symlink privileges are unavailable.
+				const directoryLinkType = process.platform === "win32" ? "junction" : "dir";
+				symlinkSync(agentsSkillsDir, agentSkillsDir, directoryLinkType);
+
+				const skillPath = join(agentsSkillsDir, "foo", "SKILL.md");
+				mkdirSync(join(agentsSkillsDir, "foo"), { recursive: true });
+				writeFileSync(skillPath, "---\nname: foo\ndescription: foo\n---\n");
+
+				const result = await packageManager.resolve();
+				const fooSkills = result.skills.filter((r) => pathEndsWith(r.path, "foo/SKILL.md"));
+
+				expect(fooSkills).toHaveLength(1);
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
 	});
 
 	describe("ignore files", () => {