fix: skip files that conflict with existing directories in FileStore.push

[octo-patch]

Fixes #1199

Problem

When the LLM generates a files dict that contains both a bare name (e.g. 'api_project') and files under a directory with the same name (e.g. 'api_project/settings.py'), the FileStore.push() method crashes with IsADirectoryError.

Root cause: when writing api_project/settings.py, path.parent.mkdir() creates the api_project/ directory. Later, when writing the file named api_project, open(path, 'w') fails because the path is now a directory.

Solution

Add a path.is_dir() check before opening the file. If the resolved path is already a directory, log a warning and skip that entry instead of raising an unhandled exception. This keeps the rest of the generated files intact and surfaces a clear diagnostic message.

Testing

The fix can be reproduced with:

from gpt_engineer.core.default.file_store import FileStore
from gpt_engineer.core.files_dict import FilesDict

store = FileStore()
# 'api_project' is both a "file" key and a directory prefix — this used to crash
files = FilesDict({
    "api_project/settings.py": "DEBUG = True",
    "api_project": "some content",
})
store.push(files)  # now skips 'api_project' with a warning instead of raising