All of the Entity Framework Migrations commands are just thin wrappers over an underlying API. To enable migrations, simply create a new class that derives from DbMigrationsConfiguration<TContext> in your project.

For Add-Migration use code similar to the following.

var config = new MyMigrationsConfiguration();
var scaffolder = new MigrationScaffolder(config);
var migration = scaffolder.Scaffold("Migration1");

File.WriteAllText(migration.MigrationId + ".cs", migration.UserCode);

File.WriteAllText(migration.MigrationId + ".Designer.cs", migration.DesignerCode);

using (var writer = new ResXResourceWriter(migration.MigrationId + ".resx"))
{
    foreach (var resource in migration.Resources)
    {
        writer.AddResource(resource.Key, resource.Value);
    }
}

For Update-Database see Running & Scripting Migrations from Code by Rowan Miller.

Update for EF 6.3 👇

A command named ef6.exe has been added to the NuGet package. It contains corresponding commands for each of the PMC commands:

|        PMC        |        ef6.exe        |
| ----------------- | --------------------- |
| Enable-Migrations | ef6 migrations enable |
| Add-Migration     | ef6 migrations add    |
| Update-Database   | ef6 database update   |
| Get-Migrations    | ef6 migrations list   |