Looks like I found a small workaround for absence of SQLite DataSource in the
list when trying to start New Connection after choosing "Update Model From
Database..." or "Generate Database from Model..." from your edmx file:

Strangely, but "SQLite Database File" data source  *exists* in the same
selection list when accessing it via 
"Tools-Connect To Database..." Visual Studio menu.

<http://sqlite.1065341.n5.nabble.com/file/n78026/Connect_to_Database.png> 

<http://sqlite.1065341.n5.nabble.com/file/n78026/Connection_to_SQLite_exists.png>
 

So first of all you can create a data connection in Visual Studio to an
SQLite file in that menu.
After that press drop-down list of existing database connections and find
that one which you have just created. After that you can proceed with your
operation.

PS. I have just found out - that after you complete this operation - "SQLite
Database File" finally appears in drop-down selection list even when you try
to access it via edmx model context menu:

<http://sqlite.1065341.n5.nabble.com/file/n78026/Finally_Appeared.png> 





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