scripts/openbabel-python.i: Revert shared_ptr changes

This reverts part of ce178cbbd3182aa3ef5729d2133f497248cf5250.
Reset maximum InChI size to 65534 as suggested by Maciek.
Fix for earlier commit to restore MCDLformat functionality
- implementBondStereo added back to mcdlutil.cpp.
Updating gaff results for testcase. These were failing since Roger's updates for MDL Valence.
Update Java, Perl and Python bindings to work without Eigen installed. More bindings to come.~
Ensure that the OBAlign tests are built for either EIGEN2 or EIGEN3
Fix problems compiling JSON formats with MSVC
* OBAPI should not be used with template classes such as OBPairTemplate
added R swig interface

all compiles now
added README, a test file and an example R package
Add R to ALL_BINDINGS, fix EIGEN dependancy issue.

The forcefield.h file causes a build error if the EIGEN
library is not included, so I move it into the
HAVE_EIGEN section in the openbabe-R.i file.
Merge branch 'khoran-R-script'