install_tree, copy_tree can install into existing directory structures (#8289)

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.

var/spack/repos/builtin/packages/snphylo/package.py

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import distutils.dir_util
 
 
 class Snphylo(Package):
@@ -51,7 +50,7 @@ def install(self, spec, prefix):
         with open(install_answer_input, 'r') as f:
             bash = which('bash')
             bash('./setup.sh', input=f)
-            distutils.dir_util.copy_tree(".", prefix)
+            install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PATH', self.spec.prefix)