I know you can change it using cscript.exe on Windows. Is there a Linux program providing cscript-like functionality? Or is there some other way I can change the database in Linux?
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CScript is just the script execution engine; it knows nothing about MSI directly. Check out Wine; it implements some/most of msi.dll, so as long as functions like MsiDatabaseOpenView and MsiViewExecute are correctly implemented, you should be able to use it to modify an .msi package.