fix(coding-agent): dedupe symlinked resources (#3818)

* fix(coding-agent): dedupe symlinked resources

Fixes #3767

* refactor(coding-agent): extract canonicalizePath util for symlink resolution

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

@@ -1,15 +1,6 @@
 import { type ChildProcess, type ChildProcessByStdio, spawn, spawnSync } from "node:child_process";
 import { createHash } from "node:crypto";
-import {
-	existsSync,
-	mkdirSync,
-	readdirSync,
-	readFileSync,
-	realpathSync,
-	rmSync,
-	statSync,
-	writeFileSync,
-} from "node:fs";
+import { existsSync, mkdirSync, readdirSync, readFileSync, 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";
@@ -18,7 +9,7 @@ import ignore from "ignore";
 import { minimatch } from "minimatch";
 import { CONFIG_DIR_NAME } from "../config.js";
 import { type GitSource, parseGitUrl } from "../utils/git.js";
-import { isLocalPath } from "../utils/paths.js";
+import { canonicalizePath, isLocalPath } from "../utils/paths.js";
 import { isStdoutTakenOver } from "./output-guard.js";
 import type { PackageSource, SettingsManager } from "./settings-manager.js";
 
@@ -2286,40 +2277,30 @@ export class DefaultPackageManager implements PackageManager {
 	}
 
 	private toResolvedPaths(accumulator: ResourceAccumulator): ResolvedPaths {
-		const toResolved = (entries: Map<string, { metadata: PathMetadata; enabled: boolean }>): ResolvedResource[] => {
+		const mapToResolved = (
+			entries: Map<string, { metadata: PathMetadata; enabled: boolean }>,
+		): ResolvedResource[] => {
 			const resolved = Array.from(entries.entries()).map(([path, { metadata, enabled }]) => ({
 				path,
 				enabled,
 				metadata,
 			}));
 			resolved.sort((a, b) => resourcePrecedenceRank(a.metadata) - resourcePrecedenceRank(b.metadata));
-			return resolved;
+
+			const seen = new Set<string>();
+			return resolved.filter((entry) => {
+				const canonicalPath = canonicalizePath(entry.path);
+				if (seen.has(canonicalPath)) return false;
+				seen.add(canonicalPath);
+				return true;
+			});
 		};
 
-		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: resolvedSkills,
-			prompts: toResolved(accumulator.prompts),
-			themes: toResolved(accumulator.themes),
+			extensions: mapToResolved(accumulator.extensions),
+			skills: mapToResolved(accumulator.skills),
+			prompts: mapToResolved(accumulator.prompts),
+			themes: mapToResolved(accumulator.themes),
 		};
 	}
 

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

@@ -8,7 +8,7 @@ import type { ResourceDiagnostic } from "./diagnostics.js";
 
 export type { ResourceCollision, ResourceDiagnostic } from "./diagnostics.js";
 
-import { isLocalPath } from "../utils/paths.js";
+import { canonicalizePath, isLocalPath } from "../utils/paths.js";
 import { createEventBus, type EventBus } from "./event-bus.js";
 import { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from "./extensions/loader.js";
 import type { Extension, ExtensionFactory, ExtensionRuntime, LoadExtensionsResult } from "./extensions/types.js";
@@ -664,8 +664,9 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		for (const p of [...primary, ...additional]) {
 			const resolved = this.resolveResourcePath(p);
-			if (seen.has(resolved)) continue;
-			seen.add(resolved);
+			const canonicalPath = canonicalizePath(resolved);
+			if (seen.has(canonicalPath)) continue;
+			seen.add(canonicalPath);
 			merged.push(resolved);
 		}
 

packages/coding-agent/src/core/skills.ts

@@ -1,9 +1,10 @@
-import { existsSync, readdirSync, readFileSync, realpathSync, statSync } from "fs";
+import { existsSync, readdirSync, readFileSync, statSync } from "fs";
 import ignore from "ignore";
 import { homedir } from "os";
 import { basename, dirname, isAbsolute, join, relative, resolve, sep } from "path";
 import { CONFIG_DIR_NAME, getAgentDir } from "../config.js";
 import { parseFrontmatter } from "../utils/frontmatter.js";
+import { canonicalizePath } from "../utils/paths.js";
 import type { ResourceDiagnostic } from "./diagnostics.js";
 import { createSyntheticSourceInfo, type SourceInfo } from "./source-info.js";
 
@@ -416,12 +417,7 @@ export function loadSkills(options: LoadSkillsOptions): LoadSkillsResult {
 		allDiagnostics.push(...result.diagnostics);
 		for (const skill of result.skills) {
 			// Resolve symlinks to detect duplicate files
-			let realPath: string;
-			try {
-				realPath = realpathSync(skill.filePath);
-			} catch {
-				realPath = skill.filePath;
-			}
+			const realPath = canonicalizePath(skill.filePath);
 
 			// Skip silently if we've already loaded this exact file (via symlink)
 			if (realPathSet.has(realPath)) {