Merge trunk into branch automake. #28588

Conflicts:
	src/Makefile
	src/Makefile_GNU
	src/cndo/Cndo2.cpp
	src/mndo/Mndo.cpp
	src/optimization/BFGS.cpp
	src/wrappers/Blas.cpp
	src/wrappers/Lapack.cpp
	src/zindo/ZindoS.cpp
Check mkl_lapacke.h. #28588
Change final output file name. #28588
Copy source file list into Makefile.am from trunk. #28588
Generate files by autoreconf 2.69 with automake 1.11.6. #28588