I have just updated from SQLite 1.0.8x to sqlite 126.96.36.199 to try and use with EF6.
When I try and add a entity data model from an existing database there is no option to select the data source as sqlite as there used to be for the older SQLite. I have installed SQLite from Nuget and from the setup file on the SQLite website for .net4.5/VS2012. I have tried reinstalling and rebooting both VS and my machine and neither worked. I have found many similar problems to this and no answers to this problem. I can add a connection to an SQLite file via server explorer and navigate through the db on the tab in Visual Studio. This now existing connection does not appear when trying to add a new model in EF6, however.
I even found this question on SO that seems to be the same question as mine but has no answers:
It seems strange to me that this issue would exist with no answers/concern about it. Are people shunning the SQLite/EF6 combo? I had EF5 and SQLite running fine.
I know this is technically a duplicate but I do not know what else I can do.
I don't know if this actually solves your issue, but I had the same problem and tried pretty much every solution out there.
Eventually, after installing the correct packages to support VS2012, I also installed Entity Framework 6 Tools for Visual Studio 2012 & 2013
After doing so (and a restart of VS) the connection showed up in the Entity Data Model Wizard.
Hope it solves your issue as well.