domain.com/file1 domain.com/file2 domain.com/file2/file2a domain.com/file2/file2b domain.com/file3
<a href="[[~[[+id]]]]">[[+pagetitle]]</a>
<a href="[[~[[+id]]? &scheme=`full`]]">[[+pagetitle]]</a>
domain.com/file2a.html
domain.com/file2/file2a.html
Just a thought have you enabled Use Friendly Alias Path (use_alias_path) within the Friendly URL System settings. That should show the full path to the resource.
Are these parents files or folders? And, are they resources or files?
domain.com/file2/file2/file2a.html