[IMP-dev] Cleanup of config/build/install script

[Daniel Russel <drussel@salilab.org>]

I just committed a cleanup of the config/build/install scripts following 
comments and patches posted previously. The changes have the following 
user-visible consequences:
new arguments added to scons:
- cxxflags, ldflags which allow the addition of arbitrary compile and 
link flags
- pythonpath which allows dirs to be added to the python path


linking has been changed as follows:
- on a mac the library ids are now set properly, both for when the 
libraries are in build/lib and when they are in installed. This means 
that you can link against them without hassle once installed. It also 
means that you just have to have PYTHONPATH set properly in order to use IMP
- search paths orderings should be consistent everywhere
- on linux, unusual directories containing libraries (i.e. things passed 
in the libflags argument) are added to the libraries runtime search 
path. This makes it less likely that a library is linked against one 
external library and run against another, as was easily the case before.
imppy.sh has been changed as follows:
- the local paths are prepended to the search path, not appended, so 
local copies of IMP will hide ones elsewhere on the system
- external LD_LIBRARY_FLAGS and PYTHONPATH and no longer propagated from 
the environment (but things can be added to them via scons). This means 
that "scons test" runs tests in the same environment as if you run the 
tests yourself with ./bin/imppy.sh
- on a mac, LD_LIBRARY_FLAGS is not set as it is no longer needed

I have tested everything on my linux box and mac, so I am reasonably 
confident that they should work. But please report any new problems 
promptly. And hopefully any issues with other platforms should be 
cleared up by Monday.
Unfortunately, it is still not possible to use the diva copy of modeller 
as the modeller test scripts are kind of strange and I didn't feel like 
messing with them. Likewise, since EMBed doesn't have a proper 
installer, it is still a special case.