Deactivation of non-native modules

[marionf]

Describe the bug

The feature to Disable non-native modules in the auto-upgrade module is not working.
⚠️ The feature to disable non native-in modules in the Advanced parameters > Performance page is also not working and should be fixed before.

According to @Progi1984 it's because it's looking for information in the install folder which must be renamed or deleted after installing PS.
@eternoendless said that we should rather use the composer.json to disable all non native-in modules

Expected behavior

As a user making an upgrade, I want to be able to disable my non native-in modules before the upgrade to ensure its success.

When the option is enabled, we should identify native modules in the destination version, then disable all modules in the current version that aren't found on that list to prevent them to crash the upgrade or the store once the upgrade has been done.

Mockups: https://www.figma.com/file/GpRsUUCHcdhJPAaz7Eqzes/Autoupgrade?node-id=497%3A11710

Steps to Reproduce

Steps to reproduce the behavior:

1. Install & configure the auto-upgrade module
2. Put "Disable non-native modules" on "Yes"
3. Go in Modules > Modules manager
4. See that non-native modules are not disabled
5. Lunch the upgrade
6. Go in Modules > Modules manager in your upgraded store
7. See that non-native modules are not disabled

[eternoendless]

To go a little further on what @marionf said, ideally we should identify native modules in the destination version, then disable all modules in the current version that aren't found on that list.

[Progi1984]

@matthieu-rolland You are now unlocked 🔓