merged changes in trunk from 2190 to 2367 into new shell branch

.gitignore

CMakeLists.txt

CTestConfig.cmake

cmake_support/OST.cmake

doc/conf/conf.py

doc/make.py

examples/dokk/datafiles/dengue/levelF.ini

examples/dokk/datafiles/dengue/top_ten.ini

examples/seq/seq_viewer.py

examples/seq/sh2.aln

examples/surf/test_rsurf.py

modules/CMakeLists.txt

modules/base/doc/base.rst

modules/base/doc/generic.rst

modules/base/pymod/CMakeLists.txt

modules/base/pymod/__init__.py

modules/base/pymod/export_logger.cc

modules/base/pymod/settings.py

modules/base/pymod/stutil.py

modules/base/pymod/wrap_base.cc