Migration Lookup source_ids array keys are not properly prefixed when creating migrations.

@mikelutz, thanks for the patch, it looks good and works just fine. I do have a few comments.

1. +++ b/src/MigrateUpgradeDrushRunner.php
   @@ -258,6 +258,14 @@ class MigrateUpgradeDrushRunner {
   +        if (isset($process['source_ids']) && is_array($process['source_ids'])) {
   

   Can we have a comment here explaining why this is needed?

2. +++ b/tests/src/Unit/MigrateUpgradeDrushRunnerTest.php
   @@ -0,0 +1,180 @@
   +            'source' => [
   +              'plugin' => 'my_source_plugin',
   +            ],
   

   Not really needed in the test, the runner doesn't change the source values. Let's keep this simple.

3. +++ b/tests/src/Unit/MigrateUpgradeDrushRunnerTest.php
   @@ -0,0 +1,180 @@
   +            'destination' => [
   +              'plugin' => 'my_destination',
   +            ],
   

   Ditto.

4. +++ b/tests/src/Unit/MigrateUpgradeDrushRunnerTest.php
   @@ -0,0 +1,180 @@
   +            'migration_dependencies' => [
   +              'required' => ['required_dependency'],
   +              'optional' => ['optional_dependency'],
   

   But here let's add a previous migration as a dependency for both required and optional and test that they are updated with the prefix as well.

5. +++ b/tests/src/Unit/MigrateUpgradeDrushRunnerTest.php
   @@ -0,0 +1,180 @@
   +  use Drupal\migrate_upgrade\MigrateUpgradeDrushRunner;
   

   The indentation on the whole class has an extra two spaces.

6. +++ b/tests/src/Unit/MigrateUpgradeDrushRunnerTest.php
   @@ -0,0 +1,180 @@
   +  class TestMigrateUpgradeDrushRunner extends MigrateUpgradeDrushRunner {
   

   Don't we have a requirement that there is one class per file? See Object-oriented code.

7. +++ b/tests/src/Unit/MigrateUpgradeDrushRunnerTest.php
   @@ -0,0 +1,180 @@
   +namespace Drupal\migrate_upgrade {
   

   Ah, this file is using a structure I am not familiar with, so really can't comment.

Can someone else comment about on the structure of the test file, it has two classes and two namespaces, which I am not sure about?

Decent test coverage. We can improve/adjust things over time. Looking good here. Honestly, I'm glad to see test coverage at all, although I would have asked for it if we didn't have any.