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This patch separates user preferences into a preferences.blend which is loaded independently of startup.blend. This allows the user to save preferences in the middle of a project without saving her work-in-progress as the default blend.
When Blender starts, the preferences.blend is loaded first, and then the startup.blend is loaded without preferences. Thus everything that was copied into the U global by preferences.blend remains and is not overwritten when startup.blend is loaded.
Ton told me that there was some discussion circa 2008 concerning changing what should be saved as a preference or not. For the life of me I couldn't find this discussion, if anybody can link it to me I would love to read it and update this patch accordingly.
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release/scripts/startup/bl_ui/space_userpref.py
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source/blender/blenkernel/BKE_global.h
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source/blender/blenkernel/intern/blender.c
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source/blender/blenlib/BLI_path_util.h
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source/blender/blenloader/intern/writefile.c
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source/blender/windowmanager/WM_api.h
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source/blender/windowmanager/intern/wm_files.c
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source/blender/windowmanager/intern/wm_init_exit.c
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source/blender/windowmanager/intern/wm_operators.c
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