I've had a look at the help documentation for Base 2, as well as Menial's product page, but haven't found an answer there. I've even clicked on the vacuum button and not noticed any change. What does that button do?
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DISCLAIMER : Not a Menial Base 2 person
VACUUM is a sqlite operation for defragmenting tables and tablespaces. It also helps reclaim diskspace.
It defragments all sqlite tables by copying data from the sqlite tables to a temp tablespace. The VACUUM operation will then swap out the old tablespace and use the new one. Database pages lost due to DELETEs and UPDATEs will no longer exist.
MONyog also uses sqlite tables for collecting database statistics and features a VACUUM operation.