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Running all of the existing Amiga-ported software requires you to run in the ABox mode of MorphOS. This mode offers very little memory protection because AmigaOS 3.x offered no memory protection whatsoever.
A proposed QBox mode of operation is supposed to be included in the not-yet-released 1.5 version of MorphOS. This mode will break the source code compatibility with AmigaOS and establish MorphOS as an independant entity (or dash it as a non-entity altogether).