The latest version of Sencha Touch (2.1) has built-in Web SQL support through the Ext.data.proxy.Sql class.
This provides official Web SQL support. However, it has virtually no documentation and is rather painful to use. Good starting point here: http://druckit.wordpress.com/2012/11/16/using-the-sencha-touch-2-1-sql-proxy/
I myself used it for the project and found that it does not give errors when a problem occurs. As an example, I had a problem when I sealed a sort declaration (which seems to be required, but not documented as such), and it stopped working. There were no errors. After about 5 hours, I found out the problem and it started working again.
This is painful, but it will do the job for a complete database repository.
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