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I was using ASP.NET vNext and I brought in the latest EF from nuget. When I compile the EF from nuget gets used but when I run mono overrides it with its old version. This means the assembly fails to load is I use any new APIs. The hack i found was to nuke the bundled ef from /usr/lib/4.5 and from the gac.
This also happens for Npgsql. Mono is overriding assemblies loaded manually with its own.