Apps targeting EF v5 wil have a config section reference for EF using a v5.0 assembly number like so:
<section name="entityFramework" type="System.Data.Entity.Internal.ConfigFile.EntityFrameworkSection, EntityFramework, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" requirePermission="false" />
The NuGet pkg for EF v6 should transform this reference to use a "6.0" version.
<section name="entityFramework" type="System.Data.Entity.Internal.ConfigFile.EntityFrameworkSection, EntityFramework, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" requirePermission="false" />
The NuGet pkg for EF v6 should transform this reference to use a "6.0" version.