After installing Magento 2 using the composer method, the update folder that is used to create the project with remains. I cannot see any reason to keep it after installing the composer dependencies.
Is it safe to delete?
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Best way is to make it inaccessible. That way you make sure modules that depend on the
update application to be (physically) present, still work.
This can be achieved in 2 different ways:
pubyour document root (best)
After doing this, it'd be nice to make a module which removes the inaccessible link to the update application in the admin.