fix: prefer .agents skills and repair codex symlink targets\n\nCo-Authored-By: Paperclip <noreply@paperclip.ing>

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

@@ -32,6 +32,17 @@ 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 = [
+  "../../.agents/skills",
+  "../../skills",
+  "../../../../../.agents/skills",
+  "../../../../../skills",
+];
+
+export interface PaperclipSkillEntry {
+  name: string;
+  source: string;
+}
 
 export function parseObject(value: unknown): Record<string, unknown> {
   if (typeof value !== "object" || value === null || Array.isArray(value)) {
@@ -245,6 +256,90 @@ export async function ensureAbsoluteDirectory(
   }
 }
 
+export async function listPaperclipSkillEntries(moduleDir: string): Promise<PaperclipSkillEntry[]> {
+  const entriesByName = new Map<string, PaperclipSkillEntry>();
+  const seenRoots = new Set<string>();
+
+  for (const relativePath of PAPERCLIP_SKILL_ROOT_RELATIVE_CANDIDATES) {
+    const root = path.resolve(moduleDir, relativePath);
+    if (seenRoots.has(root)) continue;
+    seenRoots.add(root);
+
+    const isDirectory = await fs.stat(root).then((stats) => stats.isDirectory()).catch(() => false);
+    if (!isDirectory) continue;
+
+    let entries: Awaited<ReturnType<typeof fs.readdir>>;
+    try {
+      entries = await fs.readdir(root, { withFileTypes: true });
+    } catch {
+      continue;
+    }
+
+    for (const entry of entries) {
+      if (!entry.isDirectory()) continue;
+      if (entriesByName.has(entry.name)) continue;
+      entriesByName.set(entry.name, {
+        name: entry.name,
+        source: path.join(root, entry.name),
+      });
+    }
+  }
+
+  return Array.from(entriesByName.values());
+}
+
+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 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 +13,15 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
   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 +65,32 @@ function codexHomeDir(): string {
   return path.join(os.homedir(), ".codex");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
+type EnsureCodexSkillsInjectedOptions = {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
+  skillsHome?: string;
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
+  skillsEntries?: Awaited<ReturnType<typeof listPaperclipSkillEntries>>;
-    if (isDir) return candidate;
+  linkSkill?: (source: string, target: string) => Promise<void>;
-  }
+};
-  return null;
-}
 
-async function ensureCodexSkillsInjected(onLog: AdapterExecutionContext["onLog"]) {
+export async function ensureCodexSkillsInjected(
-  const skillsDir = await resolvePaperclipSkillsDir();
+  onLog: AdapterExecutionContext["onLog"],
-  if (!skillsDir) return;
+  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 });
+  const linkSkill = options.linkSkill;
-  for (const entry of entries) {
+  for (const entry of skillsEntries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
     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 +12,9 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
@@ -23,10 +24,6 @@ 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 +79,9 @@ 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 +90,13 @@ export async function ensureCursorSkillsInjected(
   onLog: AdapterExecutionContext["onLog"],
   options: EnsureCursorSkillsInjectedOptions = {},
 ) {
-  const skillsDir = options.skillsDir ?? await resolvePaperclipSkillsDir();
+  const skillsEntries = options.skillsEntries
-  if (!skillsDir) return;
+    ?? (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 +108,16 @@ export async function ensureCursorSkillsInjected(
     );
     return;
   }
-
-  let entries: Dirent[];
-  try {
-    entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  } catch (err) {
-    await onLog(
-      "stderr",
-      `[paperclip] Failed to read Paperclip skills from ${skillsDir}: ${err instanceof Error ? err.message : String(err)}\n`,
-    );
-    return;
-  }
-
   const linkSkill = options.linkSkill ?? ((source: string, target: string) => fs.symlink(source, target));
-  for (const entry of entries) {
+  for (const entry of skillsEntries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
-
     try {
-      await linkSkill(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target, linkSkill);
+      if (result === "skipped") continue;
+
       await onLog(
         "stderr",
-        `[paperclip] Injected Cursor skill "${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 +12,9 @@ import {
   buildPaperclipEnv,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
   parseObject,
   redactEnvForLogs,
   renderTemplate,
@@ -29,10 +31,6 @@ 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 +71,6 @@ 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 +83,8 @@ function geminiSkillsHome(): string {
 async function ensureGeminiSkillsInjected(
   onLog: AdapterExecutionContext["onLog"],
 ): Promise<void> {
-  const skillsDir = await resolvePaperclipSkillsDir();
+  const skillsEntries = await listPaperclipSkillEntries(__moduleDir);
-  if (!skillsDir) return;
+  if (skillsEntries.length === 0) return;
 
   const skillsHome = geminiSkillsHome();
   try {
@@ -107,27 +97,16 @@ async function ensureGeminiSkillsInjected(
     return;
   }
 
-  let entries: Dirent[];
+  for (const entry of skillsEntries) {
-  try {
-    entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  } catch (err) {
-    await onLog(
-      "stderr",
-      `[paperclip] Failed to read Paperclip skills from ${skillsDir}: ${err instanceof Error ? err.message : String(err)}\n`,
-    );
-    return;
-  }
-
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
     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);
-      await onLog("stderr", `[paperclip] Linked Gemini skill: ${entry.name}\n`);
+      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 +12,9 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
@@ -20,10 +22,6 @@ 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 +48,22 @@ 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();
+  const skillsEntries = await listPaperclipSkillEntries(__moduleDir);
-  if (!skillsDir) return;
+  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 skillsEntries) {
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
     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(