> The new code is definitely correct

Not sure. There is mismatch between how COPY_FILES now deals with absolute path and how the entries are written to application.qrc.  COPY_FILES copies files given with absolute path now directly into the destination dir. But the proposed code would still write also the complete path into the file's entry.
The only file which seems absolute is ${CMAKE_CURRENT_BINARY_DIR}/webodf/webodfversion.js as inserted by updateJS.sh (so its addition recently broke things or uncovered the broken code), so look where it ends up with this patch, both in the build dir and in the application.qrc

So logic matching COPY_FILES would be:
```
    if (IS_ABSOLUTE ${FILE})
      GET_FILENAME_COMPONENT(_wwwfile ${FILE} NAME)
    else (IS_ABSOLUTE ${FILE})
      SET(_wwwfile ${FILE})
    endif (IS_ABSOLUTE ${FILE})
    file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/application.qrc "<file>www/${_wwwfile}</file>\n")
```
nativeQtClient does still not work, but that is another issue (hopefully I/someone finds interest soon to revive it, e.g. with native toolbar) :)