Let's look into making migration a two-step process, with a confirmation page with info about what is being migrated and what the consequences are. From #2281691: User interface for migration-based upgrades:

mikeryan:

Here's another consideration, however - if, say, that book module is enabled on the source site but not in D8, book hierarchies will not be migrated. It was an explicit decision early on that the upgrade process would not automatically enable modules in D8, but we do need a space somewhere for the site administrator to have the opportunity to do it. And they need info on what modules are at risk of not coming over, which we can't give them until they've submitted the credentials on the upgrade form...

mikeryan:

So, along with the question of giving administrators information on what stuff won't migrate until the relevant D8 modules are installed, there's https://www.drupal.org/node/2562073#comment-10289183. With the PHP module out of core, we will be converting php_code filters to filter_null, meaning that content using a format with the php_code filter will not display. Big WTF for anyone using php_code who didn't carefully read the release notes.

I know we'd like to have the single form, single click, but I'm feeling more and more we need to have a confirmation page that does some analysis of the source and destination sites before executing the migration. This page might:

List all source site modules that will be imported based on the current configuration.
List any D8 modules not enabled for which there is source data to import (and allow them to be enabled directly from this page?).
If the php_code filter is in use, warn that content using it will not display without either installing the contrib php module, or editing it after migration to set a different format and remove any PHP.

Thoughts?

webchick:

Well, something like that sounds absolutely fantastic to me.

So page 1: Just your DB credentials / File locations.

page 2: "Howdy, partner. It looks like you're running Drupal 7, with 46 contributed modules. You should know the following things about your site:

- EVERYTHING YOU HOLD DEAR WILL BE OVERWRITTEN. MAKE SURE YOU HAVE BACKUPS.

- PHP Code blah blah
- Foo, Bar, Baz modules don't have migrations, their stuff won't be moved over.
- something else.

[Proceed!]

We should create child issues for the different bits - confirming what modules are being migrated, showing which ones could be migrated if the right modules were enabled in D8, handling php_code...

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mikeryan created an issue. See original summary.

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This was basically done, and any further UX work should go under #2678638: [META] Usability refinements for Migrate UI.