PythonPackage builds flat installs instead of egg directories.

- Spack doesn't need eggs -- it manages its own directories

- Simplify install layout and reduce sys.path searches by installing all
  packages flat (eggs are deprecated for wheels, and this is also what
  wheels do).

- We now supply the --single-version-externally-managed argument to
  `setup.py install` for setuptools packages and setuptools.

- modify packages to only use setuptools args if setuptools is an
  immediate dependency

- Remove setuptools from packages that do not need it.

  - Some packages use setuptools *only* when certain args (likeb
    'develop' or 'bdist') are supplied to setup.py, and they specifically
    do not use setuptools for installation.

  - Spack never calls setup.py this way, so just removing the setuptools
    dependency works for these packages.

lib/spack/spack/build_systems/python.py

@@ -222,7 +222,24 @@ def install(self, spec, prefix):
 
     def install_args(self, spec, prefix):
         """Arguments to pass to install."""
-        return ['--prefix={0}'.format(prefix)]
+        args = ['--prefix={0}'.format(prefix)]
+
+        # This option causes python packages (including setuptools) NOT
+        # to create eggs or easy-install.pth files.  Instead, they
+        # install naturally into $prefix/pythonX.Y/site-packages.
+        #
+        # Eggs add an extra level of indirection to sys.path, slowing
+        # down large HPC runs.  They are also deprecated in favor of
+        # wheels, which use a normal layout when installed.
+        #
+        # Spack manages the package directory on its own by symlinking
+        # extensions into the site-packages directory, so we don't really
+        # need the .pth files or egg directories, anyway.
+        if ('py-setuptools' == spec.name or          # this is setuptools, or
+            'py-setuptools' in spec._dependencies):  # it's an immediate dep
+            args += ['--single-version-externally-managed', '--root=/']
+
+        return args
 
     def install_lib(self, spec, prefix):
         """Install all Python modules (extensions and pure Python)."""