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/clapack/package.py

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Clapack(MakefilePackage):
@@ -46,7 +45,7 @@ class Clapack(MakefilePackage):
     depends_on('atlas', when='+external-blas')
 
     def edit(self, spec, prefix):
-        install('make.inc.example', 'make.inc')
+        copy('make.inc.example', 'make.inc')
         if '+external-blas' in spec:
             make_inc = FileFilter('make.inc')
             make_inc.filter(r'^BLASLIB.*',
@@ -60,4 +59,4 @@ def build(self, spec, prefix):
         make('lib')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)