Clarify docs: skills go to the effective CODEX_HOME, not ~/.codex

The previous documentation parenthetical "(defaulting to ~/.codex/skills/)"
was misleading because Paperclip almost always sets CODEX_HOME to a
per-company managed home.  Update index.ts docs, skills.ts detail string,
and execute.ts inline comment to make the runtime path unambiguous.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

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

@@ -42,7 +42,7 @@ Notes:
 - Prompts are piped via stdin (Codex receives "-" prompt argument).
 - If instructionsFilePath is configured, Paperclip prepends that file's contents to the stdin prompt on every run.
 - Codex exec automatically applies repo-scoped AGENTS.md instructions from the active workspace. Paperclip cannot suppress that discovery in exec mode, so repo AGENTS.md files may still apply even when you only configured an explicit instructionsFilePath.
-- Paperclip injects desired local skills into $CODEX_HOME/skills/ (defaulting to ~/.codex/skills/) at execution time so Codex can discover "$paperclip" and related skills without polluting the project working directory.
+- Paperclip injects desired local skills into the effective CODEX_HOME/skills/ directory at execution time so Codex can discover "$paperclip" and related skills without polluting the project working directory. In managed-home mode (the default) this is ~/.paperclip/instances/<id>/companies/<companyId>/codex-home/skills/; when CODEX_HOME is explicitly overridden in adapter config, that override is used instead.
 - Unless explicitly overridden in adapter config, Paperclip runs Codex with a per-company managed CODEX_HOME under the active Paperclip instance and seeds auth/config from the shared Codex home (the CODEX_HOME env var, when set, or ~/.codex).
 - Some model/tool combinations reject certain effort levels (for example minimal with web search enabled).
 - When Paperclip realizes a workspace/runtime for a run, it injects PAPERCLIP_WORKSPACE_* and PAPERCLIP_RUNTIME_* env vars for agent-side tooling.

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

@@ -273,6 +273,8 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   const defaultCodexHome = resolveManagedCodexHomeDir(process.env, agent.companyId);
   const effectiveCodexHome = configuredCodexHome ?? preparedManagedCodexHome ?? defaultCodexHome;
   await fs.mkdir(effectiveCodexHome, { recursive: true });
+  // Inject skills into the same CODEX_HOME that Codex will actually run with
+  // (managed home in the default case, or an explicit override from adapter config).
   const codexSkillsDir = resolveCodexSkillsDir(effectiveCodexHome);
   await ensureCodexSkillsInjected(
     onLog,

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

@@ -31,7 +31,7 @@ async function buildCodexSkillSnapshot(
     sourcePath: entry.source,
     targetPath: null,
     detail: desiredSet.has(entry.key)
-      ? "Will be linked into $CODEX_HOME/skills/ on the next run."
+      ? "Will be linked into the effective CODEX_HOME/skills/ directory on the next run."
       : null,
     required: Boolean(entry.required),
     requiredReason: entry.requiredReason ?? null,

server/src/__tests__/codex-local-skill-sync.test.ts

@@ -43,7 +43,7 @@ describe("codex local skill sync", () => {
     expect(before.desiredSkills).toContain(paperclipKey);
     expect(before.entries.find((entry) => entry.key === paperclipKey)?.required).toBe(true);
     expect(before.entries.find((entry) => entry.key === paperclipKey)?.state).toBe("configured");
-    expect(before.entries.find((entry) => entry.key === paperclipKey)?.detail).toContain("$CODEX_HOME/skills/");
+    expect(before.entries.find((entry) => entry.key === paperclipKey)?.detail).toContain("CODEX_HOME/skills/");
   });
 
   it("does not persist Paperclip skills into CODEX_HOME during sync", async () => {