diff --git a/CHANGELOG.md b/CHANGELOG.md
index be863b7..ef10b57 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -52,6 +52,14 @@ under their entry.
   diagrams (local stdio vs HPC dispatch).
 
 ### Fixed
+- CLI config discovery now honors `./config.yaml` in the current working
+  directory at priority above the user config, matching the behavior of
+  git/ruff/pytest. Previously an empty user config written by
+  `uxarray-mcp setup` would silently shadow the repo's `config.yaml`,
+  causing `uxarray-mcp endpoints list` to print "No endpoints configured"
+  even when the project had endpoints defined. The empty-state message
+  now also names the loaded config file (or every searched path when
+  none was found) so the discovery is no longer invisible.
 - End-to-end validation of `run_scientific_agent` and `analyze_dataset`
   on local + Improv + UCAR endpoints. New harness
   (`scripts/validate_orchestrators.py`) covers six scenarios; both
diff --git a/src/uxarray_mcp/cli.py b/src/uxarray_mcp/cli.py
index 3246dca..493a2bc 100644
--- a/src/uxarray_mcp/cli.py
+++ b/src/uxarray_mcp/cli.py
@@ -26,6 +26,7 @@
 from uxarray_mcp.remote.config import (
     USER_CONFIG_PATH,
     discover_config_path,
+    discover_config_search_paths,
     load_config,
 )
 
@@ -118,8 +119,16 @@ def _user_write_target() -> Path:
 
 def cmd_endpoints_list(args: argparse.Namespace) -> int:
     cfg = load_config()
+    loaded = discover_config_path()
     if not cfg.endpoints and not cfg.endpoint_id:
-        print("No endpoints configured.")
+        if loaded is None:
+            print("No endpoints configured. No config file was found. Searched:")
+            for p in discover_config_search_paths():
+                print(f"  - {p}")
+            print("\nWrite a starter config with:  uxarray-mcp setup")
+        else:
+            print(f"No endpoints configured in {loaded}.")
+            print("\nAdd one with:  uxarray-mcp endpoints add <name> <uuid>")
         return 0
     payload: dict[str, Any] = {
         "config_path": str(discover_config_path() or ""),
diff --git a/src/uxarray_mcp/remote/config.py b/src/uxarray_mcp/remote/config.py
index 9c16c65..13897b2 100644
--- a/src/uxarray_mcp/remote/config.py
+++ b/src/uxarray_mcp/remote/config.py
@@ -18,8 +18,13 @@ def discover_config_path() -> Path | None:
 
     Order:
       1. ``$UXARRAY_MCP_CONFIG`` (explicit override)
-      2. ``~/.config/uxarray-mcp/config.yaml`` (user install)
-      3. ``./config.yaml`` (repo-root, dev/clone install)
+      2. ``./config.yaml`` (current working directory — project-local)
+      3. ``~/.config/uxarray-mcp/config.yaml`` (user install)
+      4. ``<repo_root>/config.yaml`` (editable install fallback)
+
+    Project-local (cwd) wins over the user config so that running the CLI
+    from inside a checkout uses the repo's config, even when an empty user
+    config was previously written by ``uxarray-mcp setup``.
 
     Returns ``None`` when no config file is found.
     """
@@ -29,6 +34,10 @@ def discover_config_path() -> Path | None:
         if candidate.exists():
             return candidate
 
+    cwd_config = Path.cwd() / "config.yaml"
+    if cwd_config.exists():
+        return cwd_config
+
     if USER_CONFIG_PATH.exists():
         return USER_CONFIG_PATH
 
@@ -39,6 +48,23 @@ def discover_config_path() -> Path | None:
     return None
 
 
+def discover_config_search_paths() -> list[Path]:
+    """Return the ordered list of paths discover_config_path inspects.
+
+    Useful for diagnostics — ``endpoints list`` prints this when no
+    endpoints are configured so the user can see exactly which file was
+    used or which paths were searched.
+    """
+    paths: list[Path] = []
+    env_path = os.environ.get("UXARRAY_MCP_CONFIG")
+    if env_path:
+        paths.append(Path(env_path).expanduser())
+    paths.append(Path.cwd() / "config.yaml")
+    paths.append(USER_CONFIG_PATH)
+    paths.append(Path(__file__).resolve().parent.parent.parent.parent / "config.yaml")
+    return paths
+
+
 _VALID_EXECUTION_MODES = {"local", "hpc", "auto"}
 _EXECUTION_MODE_ALIASES = {"remote": "hpc"}
 
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 0ebfbec..638541c 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -145,13 +145,39 @@ def test_discover_config_uses_env_var(tmp_path, monkeypatch):
     assert found == target
 
 
-def test_discover_config_user_home_beats_repo(tmp_path, monkeypatch):
+def test_discover_config_cwd_beats_user_home(tmp_path, monkeypatch):
+    """A project-local ./config.yaml takes precedence over the user config.
+
+    This prevents ``uxarray-mcp setup`` (which writes an empty user config)
+    from silently shadowing the repo's own config when the CLI is run from
+    inside a checkout.
+    """
     monkeypatch.delenv("UXARRAY_MCP_CONFIG", raising=False)
     user_cfg = tmp_path / "user.yaml"
     user_cfg.write_text("hpc: {}\n")
     monkeypatch.setattr(config_module, "USER_CONFIG_PATH", user_cfg)
-    found = config_module.discover_config_path()
-    assert found == user_cfg
+
+    cwd_dir = tmp_path / "project"
+    cwd_dir.mkdir()
+    cwd_cfg = cwd_dir / "config.yaml"
+    cwd_cfg.write_text("hpc: {execution_mode: auto}\n")
+    monkeypatch.chdir(cwd_dir)
+
+    assert config_module.discover_config_path() == cwd_cfg
+
+
+def test_discover_config_falls_back_to_user_home(tmp_path, monkeypatch):
+    """When no ./config.yaml exists, fall back to the user config."""
+    monkeypatch.delenv("UXARRAY_MCP_CONFIG", raising=False)
+    user_cfg = tmp_path / "user.yaml"
+    user_cfg.write_text("hpc: {}\n")
+    monkeypatch.setattr(config_module, "USER_CONFIG_PATH", user_cfg)
+
+    empty_dir = tmp_path / "empty"
+    empty_dir.mkdir()
+    monkeypatch.chdir(empty_dir)
+
+    assert config_module.discover_config_path() == user_cfg
 
 
 def test_discover_config_no_match_returns_none(tmp_path, monkeypatch):