I noticed that this was an issue with 1.0.93, too, but it seems to also apply to 1.0.94.
More specifically:
Make sure your system.data section looks like this:
<system.data>
<DbProviderFactories>
<remove invariant="System.Data.SQLite" />
<remove invariant="System.Data.SQLite.EF6" />
<add name="SQLite Data Provider (Entity Framework 6)" invariant="System.Data.SQLite.EF6" description=".NET Framework Data Provider for SQLite (Entity Framework 6)" type="System.Data.SQLite.EF6.SQLiteProviderFactory, System.Data.SQLite.EF6" />
</DbProviderFactories>
</system.data>