fix: only treat .specify as engine-owned when it is a real directory

A file or symlink named .specify should not be excluded from the
non-empty check. Use entry.is_dir(follow_symlinks=False) to ensure
only an actual directory is considered engine-owned content.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: mnriem

src/specify_cli/workflows/steps/init/__init__.py

@@ -129,7 +129,11 @@ def execute(self, config: dict[str, Any], context: StepContext) -> StepResult:
             try:
                 with os.scandir(base) as it:
                     has_non_engine_content = any(
-                        entry.name not in _ENGINE_OWNED_DIRS for entry in it
+                        not (
+                            entry.name in _ENGINE_OWNED_DIRS
+                            and entry.is_dir(follow_symlinks=False)
+                        )
+                        for entry in it
                     )
             except OSError as exc:
                 error_message = (