Provide some input filters for making links, along with an optional CKEditor plugin.
In two words, you can either write one of:
html <a href="entity:node/12">Some entity</a>
html <a href="entity://node/12">Some entity</a>
html <a href="{{node/12}}">Some entity</a>
in any text that would be php check_markup()
'ed and filters will be
processed and turned into correct Drupal URL or URL aliases.
The CKEditor plugin requires ckeditor >= 4.
You may use url('entity://node/12')
to generate the node link, there
is an hook_url_outbound_alter
implementation that will do the job.