Merge pull request #794 from paperclipai/split/agent-skill-resolution

fix(adapters): resolve local agent skill lookup after .agents migration

cli/src/commands/client/agent.ts

@@ -1,5 +1,9 @@
 import { Command } from "commander";
 import type { Agent } from "@paperclipai/shared";
+import {
+  removeMaintainerOnlySkillSymlinks,
+  resolvePaperclipSkillsDir,
+} from "@paperclipai/adapter-utils/server-utils";
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
@@ -34,15 +38,12 @@ interface SkillsInstallSummary {
   tool: "codex" | "claude";
   target: string;
   linked: string[];
+  removed: string[];
   skipped: string[];
   failed: Array<{ name: string; error: string }>;
 }
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../../../../skills"), // dev: cli/src/commands/client -> repo root/skills
-  path.resolve(process.cwd(), "skills"),
-];
 
 function codexSkillsHome(): string {
   const fromEnv = process.env.CODEX_HOME?.trim();
@@ -56,14 +57,6 @@ function claudeSkillsHome(): string {
   return path.join(base, "skills");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 async function installSkillsForTarget(
   sourceSkillsDir: string,
   targetSkillsDir: string,
@@ -73,20 +66,65 @@ async function installSkillsForTarget(
     tool,
     target: targetSkillsDir,
     linked: [],
+    removed: [],
     skipped: [],
     failed: [],
   };
 
   await fs.mkdir(targetSkillsDir, { recursive: true });
   const entries = await fs.readdir(sourceSkillsDir, { withFileTypes: true });
+  summary.removed = await removeMaintainerOnlySkillSymlinks(
+    targetSkillsDir,
+    entries.filter((entry) => entry.isDirectory()).map((entry) => entry.name),
+  );
   for (const entry of entries) {
     if (!entry.isDirectory()) continue;
     const source = path.join(sourceSkillsDir, entry.name);
     const target = path.join(targetSkillsDir, entry.name);
     const existing = await fs.lstat(target).catch(() => null);
     if (existing) {
-      summary.skipped.push(entry.name);
-      continue;
+      if (existing.isSymbolicLink()) {
+        let linkedPath: string | null = null;
+        try {
+          linkedPath = await fs.readlink(target);
+        } catch (err) {
+          await fs.unlink(target);
+          try {
+            await fs.symlink(source, target);
+            summary.linked.push(entry.name);
+            continue;
+          } catch (linkErr) {
+            summary.failed.push({
+              name: entry.name,
+              error:
+                err instanceof Error && linkErr instanceof Error
+                  ? `${err.message}; then ${linkErr.message}`
+                  : err instanceof Error
+                    ? err.message
+                    : `Failed to recover broken symlink: ${String(err)}`,
+            });
+            continue;
+          }
+        }
+
+        const resolvedLinkedPath = path.isAbsolute(linkedPath)
+          ? linkedPath
+          : path.resolve(path.dirname(target), linkedPath);
+        const linkedTargetExists = await fs
+          .stat(resolvedLinkedPath)
+          .then(() => true)
+          .catch(() => false);
+
+        if (!linkedTargetExists) {
+          await fs.unlink(target);
+        } else {
+          summary.skipped.push(entry.name);
+          continue;
+        }
+      } else {
+        summary.skipped.push(entry.name);
+        continue;
+      }
     }
 
     try {
@@ -210,7 +248,7 @@ export function registerAgentCommands(program: Command): void {
 
           const installSummaries: SkillsInstallSummary[] = [];
           if (opts.installSkills !== false) {
-            const skillsDir = await resolvePaperclipSkillsDir();
+            const skillsDir = await resolvePaperclipSkillsDir(__moduleDir, [path.resolve(process.cwd(), "skills")]);
             if (!skillsDir) {
               throw new Error(
                 "Could not locate local Paperclip skills directory. Expected ./skills in the repo checkout.",
@@ -258,7 +296,7 @@ export function registerAgentCommands(program: Command): void {
           if (installSummaries.length > 0) {
             for (const summary of installSummaries) {
               console.log(
-                `${summary.tool}: linked=${summary.linked.length} skipped=${summary.skipped.length} failed=${summary.failed.length} target=${summary.target}`,
+                `${summary.tool}: linked=${summary.linked.length} removed=${summary.removed.length} skipped=${summary.skipped.length} failed=${summary.failed.length} target=${summary.target}`,
               );
               for (const failed of summary.failed) {
                 console.log(`  failed ${failed.name}: ${failed.error}`);

packages/adapter-utils/src/server-utils.ts

@@ -32,6 +32,23 @@ export const runningProcesses = new Map<string, RunningProcess>();
 export const MAX_CAPTURE_BYTES = 4 * 1024 * 1024;
 export const MAX_EXCERPT_BYTES = 32 * 1024;
 const SENSITIVE_ENV_KEY = /(key|token|secret|password|passwd|authorization|cookie)/i;
+const PAPERCLIP_SKILL_ROOT_RELATIVE_CANDIDATES = [
+  "../../skills",
+  "../../../../../skills",
+];
+
+export interface PaperclipSkillEntry {
+  name: string;
+  source: string;
+}
+
+function normalizePathSlashes(value: string): string {
+  return value.replaceAll("\\", "/");
+}
+
+function isMaintainerOnlySkillTarget(candidate: string): boolean {
+  return normalizePathSlashes(candidate).includes("/.agents/skills/");
+}
 
 export function parseObject(value: unknown): Record<string, unknown> {
   if (typeof value !== "object" || value === null || Array.isArray(value)) {
@@ -245,6 +262,136 @@ export async function ensureAbsoluteDirectory(
   }
 }
 
+export async function resolvePaperclipSkillsDir(
+  moduleDir: string,
+  additionalCandidates: string[] = [],
+): Promise<string | null> {
+  const candidates = [
+    ...PAPERCLIP_SKILL_ROOT_RELATIVE_CANDIDATES.map((relativePath) => path.resolve(moduleDir, relativePath)),
+    ...additionalCandidates.map((candidate) => path.resolve(candidate)),
+  ];
+  const seenRoots = new Set<string>();
+
+  for (const root of candidates) {
+    if (seenRoots.has(root)) continue;
+    seenRoots.add(root);
+    const isDirectory = await fs.stat(root).then((stats) => stats.isDirectory()).catch(() => false);
+    if (isDirectory) return root;
+  }
+
+  return null;
+}
+
+export async function listPaperclipSkillEntries(
+  moduleDir: string,
+  additionalCandidates: string[] = [],
+): Promise<PaperclipSkillEntry[]> {
+  const root = await resolvePaperclipSkillsDir(moduleDir, additionalCandidates);
+  if (!root) return [];
+
+  try {
+    const entries = await fs.readdir(root, { withFileTypes: true });
+    return entries
+      .filter((entry) => entry.isDirectory())
+      .map((entry) => ({
+        name: entry.name,
+        source: path.join(root, entry.name),
+      }));
+  } catch {
+    return [];
+  }
+}
+
+export async function readPaperclipSkillMarkdown(
+  moduleDir: string,
+  skillName: string,
+): Promise<string | null> {
+  const normalized = skillName.trim().toLowerCase();
+  if (!normalized) return null;
+
+  const entries = await listPaperclipSkillEntries(moduleDir);
+  const match = entries.find((entry) => entry.name === normalized);
+  if (!match) return null;
+
+  try {
+    return await fs.readFile(path.join(match.source, "SKILL.md"), "utf8");
+  } catch {
+    return null;
+  }
+}
+
+export async function ensurePaperclipSkillSymlink(
+  source: string,
+  target: string,
+  linkSkill: (source: string, target: string) => Promise<void> = (linkSource, linkTarget) =>
+    fs.symlink(linkSource, linkTarget),
+): Promise<"created" | "repaired" | "skipped"> {
+  const existing = await fs.lstat(target).catch(() => null);
+  if (!existing) {
+    await linkSkill(source, target);
+    return "created";
+  }
+
+  if (!existing.isSymbolicLink()) {
+    return "skipped";
+  }
+
+  const linkedPath = await fs.readlink(target).catch(() => null);
+  if (!linkedPath) return "skipped";
+
+  const resolvedLinkedPath = path.resolve(path.dirname(target), linkedPath);
+  if (resolvedLinkedPath === source) {
+    return "skipped";
+  }
+
+  const linkedPathExists = await fs.stat(resolvedLinkedPath).then(() => true).catch(() => false);
+  if (linkedPathExists) {
+    return "skipped";
+  }
+
+  await fs.unlink(target);
+  await linkSkill(source, target);
+  return "repaired";
+}
+
+export async function removeMaintainerOnlySkillSymlinks(
+  skillsHome: string,
+  allowedSkillNames: Iterable<string>,
+): Promise<string[]> {
+  const allowed = new Set(Array.from(allowedSkillNames));
+  try {
+    const entries = await fs.readdir(skillsHome, { withFileTypes: true });
+    const removed: string[] = [];
+    for (const entry of entries) {
+      if (allowed.has(entry.name)) continue;
+
+      const target = path.join(skillsHome, entry.name);
+      const existing = await fs.lstat(target).catch(() => null);
+      if (!existing?.isSymbolicLink()) continue;
+
+      const linkedPath = await fs.readlink(target).catch(() => null);
+      if (!linkedPath) continue;
+
+      const resolvedLinkedPath = path.isAbsolute(linkedPath)
+        ? linkedPath
+        : path.resolve(path.dirname(target), linkedPath);
+      if (
+        !isMaintainerOnlySkillTarget(linkedPath) &&
+        !isMaintainerOnlySkillTarget(resolvedLinkedPath)
+      ) {
+        continue;
+      }
+
+      await fs.unlink(target);
+      removed.push(entry.name);
+    }
+
+    return removed;
+  } catch {
+    return [];
+  }
+}
+
 export async function ensureCommandResolvable(command: string, cwd: string, env: NodeJS.ProcessEnv) {
   const resolved = await resolveCommandPath(command, cwd, env);
   if (resolved) return;

packages/adapters/codex-local/src/server/execute.ts

@@ -13,17 +13,16 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
 import { parseCodexJsonl, isCodexUnknownSessionError } from "./parse.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),         // published: <pkg>/dist/server/ -> <pkg>/skills/
-  path.resolve(__moduleDir, "../../../../../skills"), // dev: src/server/ -> repo root/skills/
-];
 const CODEX_ROLLOUT_NOISE_RE =
   /^\d{4}-\d{2}-\d{2}T[^\s]+\s+ERROR\s+codex_core::rollout::list:\s+state db missing rollout path for thread\s+[a-z0-9-]+$/i;
 
@@ -67,33 +66,42 @@ function codexHomeDir(): string {
   return path.join(os.homedir(), ".codex");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
+type EnsureCodexSkillsInjectedOptions = {
+  skillsHome?: string;
+  skillsEntries?: Awaited<ReturnType<typeof listPaperclipSkillEntries>>;
+  linkSkill?: (source: string, target: string) => Promise<void>;
+};
 
-async function ensureCodexSkillsInjected(onLog: AdapterExecutionContext["onLog"]) {
-  const skillsDir = await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+export async function ensureCodexSkillsInjected(
+  onLog: AdapterExecutionContext["onLog"],
+  options: EnsureCodexSkillsInjectedOptions = {},
+) {
+  const skillsEntries = options.skillsEntries ?? await listPaperclipSkillEntries(__moduleDir);
+  if (skillsEntries.length === 0) return;
 
-  const skillsHome = path.join(codexHomeDir(), "skills");
+  const skillsHome = options.skillsHome ?? path.join(codexHomeDir(), "skills");
   await fs.mkdir(skillsHome, { recursive: true });
-  const entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    skillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
+    await onLog(
+      "stderr",
+      `[paperclip] Removed maintainer-only Codex skill "${skillName}" from ${skillsHome}\n`,
+    );
+  }
+  const linkSkill = options.linkSkill;
+  for (const entry of skillsEntries) {
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
 
     try {
-      await fs.symlink(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target, linkSkill);
+      if (result === "skipped") continue;
+
       await onLog(
         "stderr",
-        `[paperclip] Injected Codex skill "${entry.name}" into ${skillsHome}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Codex skill "${entry.name}" into ${skillsHome}\n`,
       );
     } catch (err) {
       await onLog(

packages/adapters/codex-local/src/server/index.ts

@@ -1,4 +1,4 @@
-export { execute } from "./execute.js";
+export { execute, ensureCodexSkillsInjected } from "./execute.js";
 export { testEnvironment } from "./test.js";
 export { parseCodexJsonl, isCodexUnknownSessionError } from "./parse.js";
 import type { AdapterSessionCodec } from "@paperclipai/adapter-utils";

packages/adapters/cursor-local/src/server/execute.ts

@@ -1,5 +1,4 @@
 import fs from "node:fs/promises";
-import type { Dirent } from "node:fs";
 import os from "node:os";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
@@ -13,7 +12,10 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
@@ -23,10 +25,6 @@ import { normalizeCursorStreamLine } from "../shared/stream.js";
 import { hasCursorTrustBypassArg } from "../shared/trust.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),
-  path.resolve(__moduleDir, "../../../../../skills"),
-];
 
 function firstNonEmptyLine(text: string): string {
   return (
@@ -82,16 +80,9 @@ function cursorSkillsHome(): string {
   return path.join(os.homedir(), ".cursor", "skills");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 type EnsureCursorSkillsInjectedOptions = {
   skillsDir?: string | null;
+  skillsEntries?: Array<{ name: string; source: string }>;
   skillsHome?: string;
   linkSkill?: (source: string, target: string) => Promise<void>;
 };
@@ -100,8 +91,13 @@ export async function ensureCursorSkillsInjected(
   onLog: AdapterExecutionContext["onLog"],
   options: EnsureCursorSkillsInjectedOptions = {},
 ) {
-  const skillsDir = options.skillsDir ?? await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+  const skillsEntries = options.skillsEntries
+    ?? (options.skillsDir
+      ? (await fs.readdir(options.skillsDir, { withFileTypes: true }))
+          .filter((entry) => entry.isDirectory())
+          .map((entry) => ({ name: entry.name, source: path.join(options.skillsDir!, entry.name) }))
+      : await listPaperclipSkillEntries(__moduleDir));
+  if (skillsEntries.length === 0) return;
 
   const skillsHome = options.skillsHome ?? cursorSkillsHome();
   try {
@@ -113,31 +109,26 @@ export async function ensureCursorSkillsInjected(
     );
     return;
   }
-
-  let entries: Dirent[];
-  try {
-    entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  } catch (err) {
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    skillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
     await onLog(
       "stderr",
-      `[paperclip] Failed to read Paperclip skills from ${skillsDir}: ${err instanceof Error ? err.message : String(err)}\n`,
+      `[paperclip] Removed maintainer-only Cursor skill "${skillName}" from ${skillsHome}\n`,
     );
-    return;
   }
-
   const linkSkill = options.linkSkill ?? ((source: string, target: string) => fs.symlink(source, target));
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  for (const entry of skillsEntries) {
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
-
     try {
-      await linkSkill(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target, linkSkill);
+      if (result === "skipped") continue;
+
       await onLog(
         "stderr",
-        `[paperclip] Injected Cursor skill "${entry.name}" into ${skillsHome}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Cursor skill "${entry.name}" into ${skillsHome}\n`,
       );
     } catch (err) {
       await onLog(

packages/adapters/gemini-local/src/server/execute.ts

@@ -12,7 +12,10 @@ import {
   buildPaperclipEnv,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   parseObject,
   redactEnvForLogs,
   renderTemplate,
@@ -29,10 +32,6 @@ import {
 import { firstNonEmptyLine } from "./utils.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),
-  path.resolve(__moduleDir, "../../../../../skills"),
-];
 
 function hasNonEmptyEnvValue(env: Record<string, string>, key: string): boolean {
   const raw = env[key];
@@ -73,14 +72,6 @@ function renderApiAccessNote(env: Record<string, string>): string {
   ].join("\n");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 function geminiSkillsHome(): string {
   return path.join(os.homedir(), ".gemini", "skills");
 }
@@ -93,8 +84,8 @@ function geminiSkillsHome(): string {
 async function ensureGeminiSkillsInjected(
   onLog: AdapterExecutionContext["onLog"],
 ): Promise<void> {
-  const skillsDir = await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+  const skillsEntries = await listPaperclipSkillEntries(__moduleDir);
+  if (skillsEntries.length === 0) return;
 
   const skillsHome = geminiSkillsHome();
   try {
@@ -106,28 +97,27 @@ async function ensureGeminiSkillsInjected(
     );
     return;
   }
-
-  let entries: Dirent[];
-  try {
-    entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  } catch (err) {
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    skillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
     await onLog(
       "stderr",
-      `[paperclip] Failed to read Paperclip skills from ${skillsDir}: ${err instanceof Error ? err.message : String(err)}\n`,
+      `[paperclip] Removed maintainer-only Gemini skill "${skillName}" from ${skillsHome}\n`,
     );
-    return;
   }
 
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  for (const entry of skillsEntries) {
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
 
     try {
-      await fs.symlink(source, target);
-      await onLog("stderr", `[paperclip] Linked Gemini skill: ${entry.name}\n`);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target);
+      if (result === "skipped") continue;
+      await onLog(
+        "stderr",
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Linked"} Gemini skill: ${entry.name}\n`,
+      );
     } catch (err) {
       await onLog(
         "stderr",

packages/adapters/pi-local/src/server/execute.ts

@@ -12,7 +12,10 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
@@ -20,10 +23,6 @@ import { isPiUnknownSessionError, parsePiJsonl } from "./parse.js";
 import { ensurePiModelConfiguredAndAvailable } from "./models.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),
-  path.resolve(__moduleDir, "../../../../../skills"),
-];
 
 const PAPERCLIP_SESSIONS_DIR = path.join(os.homedir(), ".pi", "paperclips");
 
@@ -50,34 +49,32 @@ function parseModelId(model: string | null): string | null {
   return trimmed.slice(trimmed.indexOf("/") + 1).trim() || null;
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 async function ensurePiSkillsInjected(onLog: AdapterExecutionContext["onLog"]) {
-  const skillsDir = await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+  const skillsEntries = await listPaperclipSkillEntries(__moduleDir);
+  if (skillsEntries.length === 0) return;
 
   const piSkillsHome = path.join(os.homedir(), ".pi", "agent", "skills");
   await fs.mkdir(piSkillsHome, { recursive: true });
-  
-  const entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    piSkillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
+    await onLog(
+      "stderr",
+      `[paperclip] Removed maintainer-only Pi skill "${skillName}" from ${piSkillsHome}\n`,
+    );
+  }
+
+  for (const entry of skillsEntries) {
     const target = path.join(piSkillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
 
     try {
-      await fs.symlink(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target);
+      if (result === "skipped") continue;
       await onLog(
         "stderr",
-        `[paperclip] Injected Pi skill "${entry.name}" into ${piSkillsHome}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Pi skill "${entry.name}" into ${piSkillsHome}\n`,
       );
     } catch (err) {
       await onLog(

server/src/__tests__/paperclip-skill-utils.test.ts

@@ -0,0 +1,61 @@
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import {
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
+} from "@paperclipai/adapter-utils/server-utils";
+
+async function makeTempDir(prefix: string): Promise<string> {
+  return fs.mkdtemp(path.join(os.tmpdir(), prefix));
+}
+
+describe("paperclip skill utils", () => {
+  const cleanupDirs = new Set<string>();
+
+  afterEach(async () => {
+    await Promise.all(Array.from(cleanupDirs).map((dir) => fs.rm(dir, { recursive: true, force: true })));
+    cleanupDirs.clear();
+  });
+
+  it("lists runtime skills from ./skills without pulling in .agents/skills", async () => {
+    const root = await makeTempDir("paperclip-skill-roots-");
+    cleanupDirs.add(root);
+
+    const moduleDir = path.join(root, "a", "b", "c", "d", "e");
+    await fs.mkdir(moduleDir, { recursive: true });
+    await fs.mkdir(path.join(root, "skills", "paperclip"), { recursive: true });
+    await fs.mkdir(path.join(root, ".agents", "skills", "release"), { recursive: true });
+
+    const entries = await listPaperclipSkillEntries(moduleDir);
+
+    expect(entries.map((entry) => entry.name)).toEqual(["paperclip"]);
+    expect(entries[0]?.source).toBe(path.join(root, "skills", "paperclip"));
+  });
+
+  it("removes stale maintainer-only symlinks from a shared skills home", async () => {
+    const root = await makeTempDir("paperclip-skill-cleanup-");
+    cleanupDirs.add(root);
+
+    const skillsHome = path.join(root, "skills-home");
+    const runtimeSkill = path.join(root, "skills", "paperclip");
+    const customSkill = path.join(root, "custom", "release-notes");
+    const staleMaintainerSkill = path.join(root, ".agents", "skills", "release");
+
+    await fs.mkdir(skillsHome, { recursive: true });
+    await fs.mkdir(runtimeSkill, { recursive: true });
+    await fs.mkdir(customSkill, { recursive: true });
+
+    await fs.symlink(runtimeSkill, path.join(skillsHome, "paperclip"));
+    await fs.symlink(customSkill, path.join(skillsHome, "release-notes"));
+    await fs.symlink(staleMaintainerSkill, path.join(skillsHome, "release"));
+
+    const removed = await removeMaintainerOnlySkillSymlinks(skillsHome, ["paperclip"]);
+
+    expect(removed).toEqual(["release"]);
+    await expect(fs.lstat(path.join(skillsHome, "release"))).rejects.toThrow();
+    expect((await fs.lstat(path.join(skillsHome, "paperclip"))).isSymbolicLink()).toBe(true);
+    expect((await fs.lstat(path.join(skillsHome, "release-notes"))).isSymbolicLink()).toBe(true);
+  });
+});