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The warnings and errors about updated/missing modules that you seen when comparing two platforms (prepping for migration) may be stale if you have enabled a module after the site was last verified. This could result in accidentally migrating the site to a platform with missing or wrong versions of modules, even thought the comparison tool erroneously reports that everything is okay.
1) Create two identical platforms, A and B
2) Create a site on Platform A. Enable a particular module, and then DELETE that module from platform B.
3) Migrate the site from Platform A to Platform B. Expected behavior: Aegir generates an error and blocks the migration, because Platform B is missing an enabled module. Actual behavior: Aegir goes ahead and migrates the site, which is now missing the enabled module.
I'm not sure what the solution is- perhaps re-verify the site as part of the migrate task, and if anything has changed since the previous verification, abort the migration. With this solution, the 'comparison' UI may still be stale, but it pretty much guarantees nothing unintended will happen.