[IMP-dev] quick container cleanup

[Daniel Russel <>]

I split the IMP_CONTAINER into IMP_CONTAINER (which owns the objects  
and deletes them and uses Index objects to identify them) and IMP_LIST  
which doesn't own the objects, supports deletions, uses ints as  
indexes etc. In the process I made various minor cleanups to things I  
had to touch. These include
- deleting rigidbody
- removing the is_active check from Restraint (and putting some  
asserts into Particle)
	- note that I didn't fix the various restraints or change is_active  
to is_deleted so if you deactive restraints, things will break (in a  
better way they then would break before IMHO). The fixes are easy but  
will take some time since they involve touching each restraint.
- cleaned up various documentation and header inclusion irregularities.
- created IMP/internal which contains classes which are not part of  
the API. These are also tagged with the doxygen \internal tag

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