diff --git a/paperforge/setup_wizard.py b/paperforge/setup_wizard.py
index 2e3f897b..2aced603 100644
--- a/paperforge/setup_wizard.py
+++ b/paperforge/setup_wizard.py
@@ -1642,6 +1642,8 @@ def _deploy_flat_command(
     """Deploy skills in flat .md command format (OpenCode)."""
     imported = []
     command_src = repo_root / "command"
+    if not (command_src.exists() and command_src.is_dir()):
+        command_src = repo_root / "paperforge" / "command_files"
     command_dst = vault / command_dir
     if not (command_src.exists() and command_src.is_dir()):
         return imported
@@ -1979,6 +1981,9 @@ def headless_setup(
         ]:
             text = text.replace(old, new)
         agents_dst.write_text(text, encoding="utf-8")
+        print(f"    [OK] AGENTS.md")
+    else:
+        print(f"    [WARN] AGENTS.md source not found; skipping")
 
     # =========================================================================
     # Phase 5: Create config files
@@ -2077,7 +2082,7 @@ PADDLEOCR_MODEL=PaddleOCR-VL-1.5
         "OCR dir": (pf_path / "ocr").exists(),
         "paperforge.json": pf_json.exists(),
         "Obsidian plugin": (vault / ".obsidian" / "plugins" / "paperforge" / "main.js").exists(),
-        "AGENTS.md": agents_dst.exists(),
+        "AGENTS.md": True if not agents_src.exists() else agents_dst.exists(),
     }
     failed = [k for k, v in checks.items() if not v]
     if failed:
diff --git a/pyproject.toml b/pyproject.toml
index 1d1ee052..3a31225e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,6 +53,7 @@ version = {attr = "paperforge.__version__"}
 paperforge = [
     "py.typed",
     "skills/literature-qa/prompt_deep_subagent.md",
+    "skills/literature-qa/scripts/*.md",
     "skills/literature-qa/chart-reading/*.md",
     "skills/literature-qa/chart-reading/*",
     "command_files/*.md",
diff --git a/tests/test_plugin_install_bootstrap.py b/tests/test_plugin_install_bootstrap.py
index f8eb8d5d..5ddb64c9 100644
--- a/tests/test_plugin_install_bootstrap.py
+++ b/tests/test_plugin_install_bootstrap.py
@@ -35,3 +35,15 @@ def test_setup_args_global_vault_before_subcommand() -> None:
         f"'--vault' (pos {vault_pos}) must appear before 'setup' (pos {setup_pos}) "
         "in setupArgs, because --vault is a global paperforge argument"
     )
+
+
+def test_setup_wizard_flat_command_falls_back_to_packaged_command_files() -> None:
+    """pip-installed setup must deploy OpenCode commands from packaged command_files."""
+    source = (REPO_ROOT / "paperforge" / "setup_wizard.py").read_text(encoding="utf-8")
+    assert 'repo_root / "paperforge" / "command_files"' in source
+
+
+def test_setup_wizard_does_not_fail_if_agents_md_missing() -> None:
+    """AGENTS.md is optional for pip-installed package deployments."""
+    source = (REPO_ROOT / "paperforge" / "setup_wizard.py").read_text(encoding="utf-8")
+    assert 'True if not agents_src.exists() else agents_dst.exists()' in source