When using the "Use Windows File Open/Save dialogs" option (Edit > Preferences > General > Misc.) files are saved without extension. If you have the main.py file, it will be saved as main (by default), if you have index.html it will be saved as index. Of course that you can just put the ".py" or ".html" extension at the end of the file name before pressing "Save", but it's unconfortable if you used to use the GTK+ Open/Save dialog which automatically adds the file extension.
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