Add subdir

Added the functionality that allows to copy files to subdirectories of the build target dir.
Issue: https://github.com/SeattleTestbed/common/issues/8
To verify: Create an empty directory with a few files. Create another directory. Use -a to copy from dir1 to dir2. Cross check to see that dir2 now has the contents of dir1.
To test: Add -a for build instructions as mentioned in the docstring