We have discussed this possibility during this week's dev meeting (https://youtu.be/s0Jsh1_lIjw?t=2491), and have agreed that at the very least it would be possible to enable modules from config (this is less risky than disabling/uninstalling modules, which has the risk to lead to data loss).
In Drupal 8+, this is achieved via the core.extension.yml config file. Perhaps we should similarly introduce a core.extensions.json file, or system.extensions.json, or reuse the existing system.core.json file for that.
GitHub Issue #:
5163
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