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

Merged Lars Bilke requested to merge bilke/ogs:refactor-prj-includes into master

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?
Edited by Lars Bilke