Fix #608: broken numpy build.

- Failed to catch all instances of modify_module when it was renamed
  to setup_dependent_package.

- Refactored remaining modify_module calls.

- Also modified Python's setup_dependent_package slightly: only
  creates empty site-packages directory for Python extensions now, not
  for all dependents.

lib/spack/spack/modules.py

@@ -160,8 +160,8 @@ def write(self):
         # package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(
-                self.pkg.module, extendee_spec, self.spec)
+            extendee_spec.package.setup_dependent_package(
+                self.pkg.module, self.spec)
 
         # Package-specific environment modifications
         spack_env = EnvironmentModifications()

lib/spack/spack/preferred_packages.py

@@ -150,7 +150,9 @@ def spec_has_preferred_provider(self, pkgname, provider_str):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           One version is less-than another if it is preferred over the other."""
+           Versions marked 'preferred=True' in package.py take precedence over any
+           versions not marked preferred.
+        """
         return self._spec_compare(pkgname, 'version', a, b, True, None)