The Windows installer creates a shortcut (Run SQLite utility) in the 'User Data' folder which runs this utility. The utility performs some simple input validation before starting the appropriate SQLite command-line utility (either sqlite3.exe for POPFile 1.1.0 (or later) or sqlite.exe for POPFile 0.21.0 to 1.0.1).
One of the reasons for providing runsqlite.exe is that the SQLite command-line utility (sqlite3.exe or sqlite.exe) creates an empty SQLite database without any warning if it cannot find the specified database.
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