Clarify Codex instruction sources

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

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

@@ -40,6 +40,8 @@ Operational fields:
 
 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 the active workspace's ".agents/skills" directory at execution time so Codex can discover "$paperclip" and related skills without coupling them to the user's login home.
 - 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).

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

@@ -427,16 +427,22 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
       );
     }
   }
+  const repoAgentsNote =
+    "Codex exec automatically applies repo-scoped AGENTS.md instructions from the current workspace; Paperclip does not currently suppress that discovery.";
   const commandNotes = (() => {
-    if (!instructionsFilePath) return [] as string[];
+    if (!instructionsFilePath) {
+      return [repoAgentsNote];
+    }
     if (instructionsPrefix.length > 0) {
       return [
         `Loaded agent instructions from ${instructionsFilePath}`,
         `Prepended instructions + path directive to stdin prompt (relative references from ${instructionsDir}).`,
+        repoAgentsNote,
       ];
     }
     return [
       `Configured instructionsFilePath ${instructionsFilePath}, but file could not be read; continuing without injected instructions.`,
+      repoAgentsNote,
     ];
   })();
   const bootstrapPromptTemplate = asString(config.bootstrapPromptTemplate, "");