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how to replace running executable: https://stackoverflow.com/questions/9162969/how-can-a-c-binary-replace-itself
N old versions should be kept so the user can quickly downgrade if needed. If the user wants to downgrade to a version which isn't downloaded it has to be downloaded from GitHub.
Config and cache databases should either be backwards-compatible or downgraded too if the version of the database is newer than the current version.
Running the installer is better than replacing the executable directly because the installer will do things like writing the current version into the registry. Unfortunately the user has to click through the installer for every update.
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