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Vacuuming could be useful even for gpkgs without the -wal sidecar
Vacuuming takes some time, so we should check that it is worth it.
Sources https://gdal.org/en/stable/drivers/vector/gpkg.html When dropping a table, or removing records from tables, the space they occupied is not immediately released and kept in the pool of file pages that SQLite may reuse later. If you need to shrink the file to its minimum size, you need to issue an explicit "VACUUM" SQL request.
https://sqlite.org/lang_vacuum.html When content is deleted from an SQLite database, the content is not usually erased, but rather the space used to hold the content is marked as being available for reuse.
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