I believe, this is introduced with
"(11.0.8) Svn plugin: removed the tree view and use a standard table view instead"

In the old version there was a tree item for unversioned files:

There I could add the file to the project or ignore the file via context menu on the items.

In Codelite 12 with the table view unversioned files are not listed and I have to use the command line to add or ignore items