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Because having so many separate db files is unneccessary clutter and putting tables into separate database files has an overhead in terms of query complexity and performance. Since notes supports FTS and can contain potentially large amounts of text it cannot be in metadata.db so it must be separate. Not to mention I like to develop things incrementally and doing that
wit a separate db file is much easier. And then there are considerations of backup, currently the .calnotes folder is complete including main data and backups. If I were to move some tables into metadata.db there becomes a cross dependence.
Splitting it further into a separate fts means you then need to deal with user deleteing only the fts.db and other complications. FTS is optional for the main database not for notes.
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