My solution to this problem is to add a panel/view in Dolphin where the links to files and folders can be temporarily saved for a session. The files and folders are "staged" on this panel. Hence, the user can add folders and files from several different directories to this panel and can then collectively perform actions on all the items in the tray such as copy, paste, cut, archive, rename, create list of symbolic links, etc. This makes complex file operations easy by staging the operation before performing it. This panel works very similarly to the Split view already existing in Dolphin to make additions such as drag and drop very easy.
A full description of this project with exhaustive discussion of use cases, implementation details, and user interaction model can be found here: https://goo.gl/eDnCJZ