It is possible to define a namespace for your Org. Whilst namespaces are normally associated with managed packages it is possible to define an namespace for any Org. This has the effect of prefixing any custom component in your Org with the namespace that you have provided (which must be unique in the whole Salesforce ecosystem) and '__'.
When the Org is synced to the Org Model in Elements all the custom items will appear in the Managed package part of the tree under the name given to the namespace, even though it is not a managed package.
If you add a namespace to an existing Org that has already been sync'd to Elements it will consider all of the custom components as new components, since they now have a new unique api name. The existing items which are in the main body of the tree will be marked as deleted.