The Save As… dialog, by default, creates files with no extension. When you double-click on the newly created file, the OS complains that there is no app for it.
The extension on the original file should be included.
There are two orthogonal notions here: having an extension or not, being opened with AlphaCocoa or another application.
The SaveAs dialog does respect the extension you specify: if you choose to save your file as something.foo, then your file is really saved under that name (including the extension). If you do not see the extension in the Finder, it may be because the Finder is hiding it: you can verify this in the Finder info for that file.
Last edit: Bernard Desgraupes 2016-11-28
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There are two orthogonal notions here: having an extension or not, being opened with AlphaCocoa or another application.
The SaveAs dialog does respect the extension you specify: if you choose to save your file as something.foo, then your file is really saved under that name (including the extension). If you do not see the extension in the Finder, it may be because the Finder is hiding it: you can verify this in the Finder info for that file.
Last edit: Bernard Desgraupes 2016-11-28
After verification, it seems that the Save As command works exactly as expected. Marking this ticket as
WORKSFORMEunless proved otherwise.