Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.

- `copy_tree` copies without setting permissions.  It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions.  It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.