build: generate bootstrap.h in CMAKE_BINARY_DIR

Prior to these changes bootstrap.h was generated right in the source
directory even for out of source build. Firstly such approach doesn't
respect the idea of building outside the source files. Furthermore
this leads to build failures when the source directory is located on
read-only file system.

As a result of the patch bootstrap.h is generated within the build
tree and include directories are adjusted the corresponding way.

Also changed destination build directory from source to binary path.

Part of #4968