[prj] Refactor <include> to allow additional patch run after includes.

When include and patch method in prj files are combined the logical order is the following:

1. Apply patches
2. Insert includes
3. Apply patches marked with after_includes="true"-attribute only. <-- This is new.

@ufz-bgr: Added new ogs cli parameter: --write-prj which writes the processed prj file to disk.

Fixes #3249 (closed).

1. Feature description was added to the changelog
2. Tests covering your feature were added?
3. Any new feature or behavior change was documented?