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/cp2k/package.py

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import shutil
 import copy
 
 from spack import *
@@ -266,8 +265,7 @@ def install(self, spec, prefix):
                 lib_dir = join_path('lib', cp2k_architecture, cp2k_version)
                 mkdirp(lib_dir)
                 try:
-                    shutil.copy(env['LIBSMM_PATH'],
-                                join_path(lib_dir, 'libsmm.a'))
+                    copy(env['LIBSMM_PATH'], join_path(lib_dir, 'libsmm.a'))
                 except KeyError:
                     raise KeyError('Point environment variable LIBSMM_PATH to '
                                    'the absolute path of the libsmm.a file')
@@ -315,4 +313,4 @@ def install(self, spec, prefix):
                  'VERSION={0}'.format(cp2k_version))
             env['PWD'] = pwd_backup
         exe_dir = join_path('exe', cp2k_architecture)
-        shutil.copytree(exe_dir, self.prefix.bin)
+        install_tree(exe_dir, self.prefix.bin)