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/grackle/package.py

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os.path
-import shutil
 import inspect
 
 from spack import *
@@ -78,7 +77,7 @@ def install(self, spec, prefix):
             'clib',
             'Make.mach.{0}'.format(grackle_architecture)
         )
-        shutil.copy(template, makefile)
+        copy(template, makefile)
         for key, value in substitutions.items():
             filter_file(key, value, makefile)