I downloaded and installed the last full build of GSAK to a new folder, then installed the latest update, started GSAK and imported the test data. There are 17 tables in that copy of GSAK - i.e. these are the minimum tables included in a fresh install:
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However, doing the kind of wholesale editing of the GSAK database you proposed using an external tool or direct SQLite update in a macro is not supported and will likely end in tears because neither method can take into account the internal GSAK dependencies. In other words, do NOT do that (the macro RESYNC command won't help if you inadvertently delete or damage a critical table).
If this is really an issue for you (and practically speaking, I'm not sure why it would be), backup all of your data and settings to an external location (flash drive or a folder on your PC outside the GSAK folder tree), uninstall GSAK, delete the GSAK program files folder and application data folder and subfolders. Now install the last full build and install the latest update, and restore your data and settings from the backup file you created. This will eliminate any unnecessary tables without risking any data or settings that you want to keep.

However, doing the kind of wholesale editing of the GSAK database you proposed using an external tool or direct SQLite update in a macro is not supported and will likely end in tears because neither method can take into account the internal GSAK dependencies. In other words, do NOT do that (the macro RESYNC command won't help if you inadvertently delete or damage a critical table).
If this is really an issue for you (and practically speaking, I'm not sure why it would be), backup all of your data and settings to an external location (flash drive or a folder on your PC outside the GSAK folder tree), uninstall GSAK, delete the GSAK program files folder and application data folder and subfolders. Now install the last full build and install the latest update, and restore your data and settings from the backup file you created. This will eliminate any unnecessary tables without risking any data or settings that you want to keep.