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Support custom indexes, and indexes on virtual tables
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re custom indexes:

Does not the index on expression functionality perform what you are requesting for native tables? All you have to do is to register a user defined function with the SQLITE_DETERMINISTIC flag, then 

CREATE INDEX yadayada ON tbl (my_func([<options>,*]<fields>));

allows you to use EXACTLY the same expression in the WHERE, JOIN ON and ORDER BY clauses.

https://sqlite.org/expridx.html 

re VT indexes:

The interface is already in place to index on anything you want in a virtual table, all you need do is implement xBestIndex and xFilter/xNext to cope with whatever you need.