Improve pro2cmake conversion script to keep around special case edits on regeneration

Many of our project CMakeLists.txt files have manual additions to them after they are generated by pro2cmake.py.

When they are regenerated, the manual additions are lost.

We should improve the script to keep those manual additions.
This will greatly simplify maintenance burden when we do merges from qt5/dev -> qt6/dev and have to regenerate many of the project files (developers won't have to manually resolve the conflicts again and again).