Try to get away from linking source files into the build directory

[benmwebb]

For example, we link all of module/foo/include/*.h from the source directory into include/IMP/foo/ in the build directory. We can probably avoid this and modify our install rules and compile-time -I flags accordingly.

• Avoiding links would speed up the build on Windows systems (where we can't make symlinks, so we copy instead) and greatly reduce the disk space used at build time.
• cmake 3.3 and later gets upset about files in the build directory that appeared there 'magically' (without a cmake build rule). We can appease it for now by setting the CMP0058 policy, but this will stop working eventually.