In the case of Git, I would recommend that you add rules to your .gitignore to ignore files containing sensitive information ( .hgignore for Mercurial). Try to keep confidential information in one place as much as possible (for example, a settings file). If you are working with a web map, this information is usually in a single file (for example, in Django there is a settings.py file with information about the database, secret key, etc.). If you have confidential information rooted in different parts of the application, multiply the information by some configuration file or object.
If you want people to still know where the data comes from, include an example or a dummy file with fake data with a record somewhere (either in the file or in README) that the file should be modified. Then you can name the file, for example, settings.py.example and ignore the real settings.py .
Keeping multiple repositories is a bad idea. Just leave sensitive data and make sure that you make it obvious that it is not there and that it is missing so that people can still reuse your work.
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