The 3-character limit no longer exists on Windows, so I would suggest using a longer extension, which will immediately make it clear that this is for your application. For instance. Suppose your application is called StreetBuilder, just use the .streetbuilder extension.
Beware of version issues. After a few years, you can change your file format due to the new functionality of the application. Do not be tempted to change the file format and file extensions (because in the end you get extensions such as .streetbuilder2, .streetbuilder3, ...). Instead, stick with a sequential extension (.streetbuilder) and specify the version number at the beginning of the file contents.
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