@@ -27,6 +27,7 @@
 from simple_module_cli.catalog import CATALOG, PRESETS, expand_deps
 from simple_module_cli.recipes import RECIPES, ScaffoldCtx
 from simple_module_cli.scaffolding import (
+    SAFE_PRESERVED_NAMES,
     _module_to_pypi_name,
     create_host,
     create_module,
@@ -97,38 +98,39 @@ def create_app_project(
     tenancy: bool = False,
     selected: Sequence[str] | None = None,
     flat: bool = False,
-) -> Path:
+) -> tuple[Path, list[Path]]:
     """Greenfield ``simple-module new`` scaffold.
 
-    In workspace mode (the default), lays down a uv + npm workspace at
-    ``target/`` with the host under ``target/host/`` and a sample module
-    under ``target/modules/hello/``. In flat mode (``flat=True``), keeps
-    the legacy single-host layout: host files at ``target/`` with no
-    ``modules/`` directory or workspace plumbing.
+    Workspace mode (default) lays down a uv + npm workspace at ``target/``
+    with the host under ``target/host/`` and a sample module under
+    ``target/modules/hello/``. Flat mode keeps the legacy single-host layout.
+    Tolerates ``SAFE_PRESERVED_NAMES`` at ``target`` (leftovers from
+    ``git init`` / ``gh repo create`` / IDE setup); other pre-existing
+    entries raise ``FileExistsError``.
 
-    Generates a secret, picks a DB URL, rewrites the host's
-    ``pyproject.toml`` / the relevant ``package.json`` to pin exact
-    framework versions, and applies any matching post-scaffold recipes
-    (e.g. the ``background_tasks`` recipe drops a Celery worker stack).
-
-    Returns the host directory — ``target`` in flat mode, ``target/host``
-    in workspace mode.
+    Returns ``(host_dir, preserved)`` — the host directory (``target`` in
+    flat mode, ``target/host`` in workspace mode) and the paths whose
+    scaffold copy was skipped because the user already had one.
     """
-    if target.exists() and any(target.iterdir()):
-        raise FileExistsError(
-            f"Destination {target} already exists and is non-empty; "
-            "choose a new path or remove its contents first."
-        )
-
     chosen = list(selected) if selected is not None else list(PRESETS["standard"])
     resolved, _added = expand_deps(chosen)
 
     display_names = [to_pascal_case(CATALOG[m].display) for m in resolved]
     host_dir = target if flat else target / "host"
+    preserved: list[Path] = []
     if not flat:
-        target.mkdir(parents=True, exist_ok=True)
-        create_workspace(target, name=name)
-    create_host(host_dir, name=name, modules=display_names, framework_version=_FRAMEWORK_VERSION)
+        preserved.extend(
+            create_workspace(target, name=name, preserve_existing=SAFE_PRESERVED_NAMES)
+        )
+    preserved.extend(
+        create_host(
+            host_dir,
+            name=name,
+            modules=display_names,
+            framework_version=_FRAMEWORK_VERSION,
+            preserve_existing=SAFE_PRESERVED_NAMES if flat else frozenset(),
+        )
+    )
     if not flat:
         _strip_workspace_owned_files(host_dir)
 
@@ -180,7 +182,7 @@ def create_app_project(
         if recipe_key is not None and recipe_key in RECIPES:
             RECIPES[recipe_key].apply(target, ctx)
 
-    return host_dir
+    return host_dir, preserved
 
 
 def _strip_workspace_owned_files(host_dir: Path) -> None:
 
@@ -111,7 +111,7 @@ def new_project(
             raise typer.Exit(code=1) from None
 
     try:
-        host_dir = create_app_project(
+        host_dir, preserved = create_app_project(
             target,
             name=name,
             db=db_final,
@@ -125,6 +125,14 @@ def new_project(
 
     typer.echo(f"Created app '{name}' at {target}")
     typer.echo(f"Modules: {', '.join(resolved)}")
+    if preserved:
+        typer.echo(
+            "\nPreserved existing files (scaffold's versions were skipped — "
+            "merge by hand if you want their contents):"
+        )
+        for path in preserved:
+            rel = path.relative_to(target) if path.is_relative_to(target) else path
+            typer.echo(f"  {rel}")
     typer.echo("\nNext steps:")
     typer.echo(f"  cd {target}")
     if no_install:
 
@@ -28,13 +28,28 @@
     validate_scaffold_name,
 )
 
-__all__ = ["create_host", "create_module", "create_workspace"]
+__all__ = [
+    "SAFE_PRESERVED_NAMES",
+    "create_host",
+    "create_module",
+    "create_workspace",
+]
 
 logger = logging.getLogger(__name__)
 
 _TEMPLATES_PACKAGE = "simple_module_cli.templates"
 _PACKAGE_PATH_TOKEN = "__PACKAGE__"
 
+# Pre-existing entries we tolerate at a scaffold target — typical leftovers
+# from ``git init`` / ``gh repo create`` / IDE setup.
+SAFE_PRESERVED_NAMES = frozenset(
+    {".git", ".gitignore", ".gitattributes", ".editorconfig", ".DS_Store"}
+    | {".claude", ".vscode", ".idea"}
+    | {"README", "README.md", "README.rst"}
+    | {"LICENSE", "LICENSE.md", "LICENSE.txt", "COPYING"}
+    | {"CHANGELOG.md", "CONTRIBUTING.md", "CODE_OF_CONDUCT.md"}
+)
+
 
 def _module_to_pypi_name(name: str) -> str:
     return f"simple_module_{name.lower()}"
@@ -50,12 +65,21 @@ def _iter_template_files(template_root: Path):
         yield path
 
 
-def _require_empty_dest(dest: Path) -> None:
-    if dest.exists() and any(dest.iterdir()):
-        raise FileExistsError(
-            f"Destination {dest} already exists and is non-empty. "
-            "Choose a new path or remove the contents first."
-        )
+def _require_empty_dest(dest: Path, *, preserve_existing: frozenset[str] = frozenset()) -> None:
+    """Refuse a non-empty destination unless every top-level entry is allowed.
+
+    ``preserve_existing`` is matched against the *name* of each top-level entry,
+    so callers can permit common pre-existing files (``.git``, ``README.md``,
+    ...) without silently overwriting unrelated user content.
+    """
+    if dest.exists():
+        unexpected = sorted(p.name for p in dest.iterdir() if p.name not in preserve_existing)
+        if unexpected:
+            raise FileExistsError(
+                f"Destination {dest} exists and contains files that would collide "
+                f"with the scaffold: {', '.join(unexpected)}. "
+                "Move them aside or choose another path."
+            )
     dest.mkdir(parents=True, exist_ok=True)
 
 
@@ -71,13 +95,20 @@ def _apply_template_files(
     substitutions: Mapping[str, str],
     *,
     path_rewrites: Mapping[str, str] | None = None,
-) -> None:
+    preserve_existing: frozenset[str] = frozenset(),
+) -> list[Path]:
+    """Write template files into ``dest``; return paths skipped to preserve the user's copy."""
+    preserved: list[Path] = []
     for src in _iter_template_files(src_root):
         rel_str = str(src.relative_to(src_root))
         for old, new in (path_rewrites or {}).items():
             rel_str = rel_str.replace(old, new)
         rel_str = rel_str.removesuffix(".tpl")
         target = dest / rel_str
+        top = Path(rel_str).parts[0] if rel_str else ""
+        if top in preserve_existing and target.exists():
+            preserved.append(target)
+            continue
         target.parent.mkdir(parents=True, exist_ok=True)
         if src.suffix == ".tpl":
             text = src.read_text(encoding="utf-8")
@@ -86,32 +117,41 @@ def _apply_template_files(
             target.write_text(text, encoding="utf-8")
         else:
             shutil.copy2(src, target)
+    return preserved
 
 
 def create_workspace(
     dest: Path,
     name: str,
     template_root: Path | None = None,
-) -> Path:
-    """Materialize the workspace-root shell at ``dest``.
+    *,
+    preserve_existing: frozenset[str] = frozenset(),
+) -> list[Path]:
+    """Materialize the workspace-root shell at ``dest``; return preserved paths.
 
     Lays down the top-level ``pyproject.toml`` (uv workspace), ``package.json``
     (npm workspace), ``Makefile`` (delegates to host), ``.env.example``,
     ``.gitignore``, and ``README.md``. Does NOT create the host or any
     modules — those go under ``dest/host`` and ``dest/modules/`` afterwards.
+
+    ``preserve_existing`` lists top-level entry names that may already exist
+    in ``dest``; the scaffold's copy is skipped and the preserved path is
+    included in the returned list. Other pre-existing entries raise
+    ``FileExistsError``.
     """
     dest = Path(dest)
-    dest.mkdir(parents=True, exist_ok=True)
-    _apply_template_files(
+    _require_empty_dest(dest, preserve_existing=preserve_existing)
+    preserved = _apply_template_files(
         _resolve_template_root("workspace", template_root),
         dest,
         {
             "{{HOST_NAME}}": validate_scaffold_name(name),
             "{{HOST_PYPI_NAME}}": to_kebab_case(name),
         },
+        preserve_existing=preserve_existing,
     )
     logger.info("Scaffolded workspace root at %s", dest)
-    return dest
+    return preserved
 
 
 def create_host(
@@ -120,11 +160,17 @@ def create_host(
     modules: Sequence[str],
     template_root: Path | None = None,
     framework_version: str = "*",
-) -> Path:
+    *,
+    preserve_existing: frozenset[str] = frozenset(),
+) -> list[Path]:
+    """Scaffold a host project at ``dest``; return preserved pre-existing paths.
+
+    ``preserve_existing`` semantics match :func:`create_workspace`.
+    """
     dest = Path(dest)
-    _require_empty_dest(dest)
+    _require_empty_dest(dest, preserve_existing=preserve_existing)
     module_dep_lines = "\n".join(f'    "{_module_to_pypi_name(m)}>=0.1,<1.0",' for m in modules)
-    _apply_template_files(
+    preserved = _apply_template_files(
         _resolve_template_root("host", template_root),
         dest,
         {
@@ -133,11 +179,12 @@ def create_host(
             "{{MODULE_DEPS}}": module_dep_lines,
             "{{FRAMEWORK_VERSION}}": framework_version,
         },
+        preserve_existing=preserve_existing,
     )
     logger.info(
         "Scaffolded host '%s' at %s (modules: %s)", name, dest, ", ".join(modules) or "<none>"
     )
-    return dest
+    return preserved
 
 
 def create_module(
 
@@ -0,0 +1,96 @@
+"""Regression tests for ``smpy new`` against a non-empty destination.
+
+Issue #148: scaffolding into a directory that already contains a fresh
+``git init`` (or ``gh repo create``) layout — ``.git/``, ``.gitignore``,
+``README.md``, ``LICENSE`` — has to succeed without clobbering the user's
+files. Arbitrary pre-existing entries must still hard-fail so we don't
+overwrite real work.
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from simple_module_cli.cli import app
+from typer.testing import CliRunner
+
+
+def test_sm_new_tolerates_git_init_leftovers_in_dest(tmp_path: Path) -> None:
+    """``smpy new --dest .`` after ``git init`` / ``gh repo create`` must succeed,
+    even with ``.git/``, ``.gitignore``, ``README.md``, ``LICENSE`` pre-existing —
+    the scaffold preserves them and writes everything else."""
+    runner = CliRunner()
+    target = tmp_path / "demo"
+    target.mkdir()
+    (target / ".git").mkdir()
+    user_gitignore = "*.pyc\n"
+    (target / ".gitignore").write_text(user_gitignore)
+    user_readme = "# demo (user-authored)\n"
+    (target / "README.md").write_text(user_readme)
+    (target / "LICENSE").write_text("MIT\n")
+
+    result = runner.invoke(
+        app,
+        ["new", "demo", "--yes", "--db", "sqlite", "--no-install", "--dest", str(target)],
+    )
+
+    assert result.exit_code == 0, result.output
+    assert (target / ".git").is_dir()
+    assert (target / ".gitignore").read_text() == user_gitignore
+    assert (target / "README.md").read_text() == user_readme
+    assert (target / "LICENSE").read_text() == "MIT\n"
+    assert (target / "host" / "pyproject.toml").is_file()
+    assert (target / "modules" / "hello").is_dir()
+    assert "Preserved existing files" in result.output
+    assert ".gitignore" in result.output
+    assert "README.md" in result.output
+
+
+def test_sm_new_flat_tolerates_git_init_leftovers(tmp_path: Path) -> None:
+    """Flat mode (host-at-target) must also tolerate the safe allowlist,
+    since `smpy new --flat --dest .` is the same flow against a fresh
+    `git init`."""
+    runner = CliRunner()
+    target = tmp_path / "demo"
+    target.mkdir()
+    (target / ".git").mkdir()
+    (target / ".gitignore").write_text("# user\n")
+
+    result = runner.invoke(
+        app,
+        [
+            "new",
+            "demo",
+            "--yes",
+            "--flat",
+            "--db",
+            "sqlite",
+            "--no-install",
+            "--dest",
+            str(target),
+        ],
+    )
+
+    assert result.exit_code == 0, result.output
+    assert (target / ".gitignore").read_text() == "# user\n"
+    assert (target / "pyproject.toml").is_file()
+
+
+def test_sm_new_still_refuses_unrelated_files_in_dest(tmp_path: Path) -> None:
+    """Tolerance is *narrow* — arbitrary pre-existing files (anything not in
+    the safe allowlist) must still be a hard error so users don't accidentally
+    scaffold over real work."""
+    runner = CliRunner()
+    target = tmp_path / "demo"
+    target.mkdir()
+    (target / "my_notes.md").write_text("don't clobber me")
+
+    result = runner.invoke(
+        app,
+        ["new", "demo", "--yes", "--db", "sqlite", "--no-install", "--dest", str(target)],
+    )
+
+    assert result.exit_code != 0
+    output = result.output + (result.stderr or "")
+    assert "my_notes.md" in output
+    assert (target / "my_notes.md").read_text() == "don't clobber me"