Upgrade script replaces all core-bundled plugins

[tomgreenfield]

Expected Behaviour

The upgrade script should only update a core-bundled plugin if a newer version is available and its settings in Plugin Management should remain as-is (i.e. whether it's enabled and included in new courses).

Actual Behaviour

The upgrade script replaces all plugins listed in the newly downloaded framework's adapt.json. The undesired side effects of this are:

• Newer/custom uploaded versions of plugins are overwritten e.g. a version of Spoor at 2.1.4-rc.1 is overwritten by 2.1.3.
• The plugins' database attributes isLocalPackage, _isAvailableInEditor & _isAddedByDefault are reset to their default values.

Steps to Reproduce

1. Upload a custom version of a core-bundled plugin with a higher version than the latest compatible version on GitHub.
2. Disable a few core-bundled plugins and set some to be added to new courses by default.
3. Run node upgrade allowing the framework to upgrade.
4. Check Plugin Management and see that the plugins' attributes have reset and the custom version of the earlier plugin has been replaced.

Versions

• Authoring Tool Version: 0.7.1
• Framework Version: 2.3.2 → 2.3.3
• Node.js Version: 10.11