You did mention you are using the project.json file making me believe you are using the default ASP.NET 5 template which uses EF7 .
You can verify this by looking in your project.json at the version number.
Mine for example is:
"EntityFramework.Commands": "7.0.0-beta8",
"EntityFramework.SqlServer": "7.0.0-beta8",
or in your Package Manager Console type in:
get-command -module entityframework

which will give you the available commands you can use. From the above you can see I am using Entity Framework 7.
Enable-Migrations is not listed in the commands and that is the reason you are getting the error:
The term 'Enable-Migrations' is not recognized as the name of a cmdlet
If you wish to rather use EF6 instead you would have to remove those entries in your project.json and you can add via nuget or the package manager console EF6. Just keep in mind if you use EF6 the ASP.NET 5 Identity 3 will break as it is dependent on EF7.
The command Enable-Migrations does not exist in Entity Framework 7 like it did in previous Entity framework versions.
In EF7 the task of creating the migrations folder is now combined with the Add-Migration command.
See below for the Add-Migration command differences between EF6 and EF7:
