[fix] Fix bootstrap working set order

In bootstrap we potentially copy eggs from the working set to ./eggs.
We then reconstruct the same working set using the moved locations.

This commits ensures we keep a correct working set order throughout
and that we avoid activating unintended dists.

src/zc/buildout/buildout.py

@@ -635,38 +635,56 @@ class Buildout(DictMixin):
         # nothing will be installed, but then we'll copy them to
         # the local eggs or develop-eggs folder just after this.
 
-        # Now copy buildout and setuptools eggs, and record destination eggs:
-        entries = []
+        # XXX Note: except if the current modules are not eggs, in which case
+        # we'll create .egg-link to them. This applies to packages installed
+        # in site-packages by pip (.dist-info, not .egg), which in turn would
+        # cause site-packages to be in the sys.path of the generated script.
+
+        # Sort the working set to keep entries with single dists first.
+        options = self['buildout']
+        buildout_dir = options['directory']
+        eggs_dir = options['eggs-directory']
+        develop_eggs_dir = options['develop-eggs-directory']
+        ws = zc.buildout.easy_install.sort_working_set(
+                ws,
+                buildout_dir=buildout_dir,
+                eggs_dir=eggs_dir,
+                develop_eggs_dir=develop_eggs_dir
+                )
+
+        # Now copy buildout and setuptools eggs, and record destination eggs.
+        # XXX Note: dists using .dist-info format - e.g. packages installed by
+        # pip in site-packages - will be seen as develop dists and not copied.
+        egg_entries = []
+        link_dists = []
         for dist in ws:
             if dist.precedence == pkg_resources.DEVELOP_DIST:
                 dest = os.path.join(self['buildout']['develop-eggs-directory'],
                                     dist.key + '.egg-link')
                 with open(dest, 'w') as fh:
                     fh.write(dist.location)
-                entries.append(dist.location)
+                link_dists.append(dist)
             else:
                 dest = os.path.join(self['buildout']['eggs-directory'],
                                     os.path.basename(dist.location))
-                entries.append(dest)
+                egg_entries.append(dest)
                 if not os.path.exists(dest):
                     if os.path.isdir(dist.location):
                         shutil.copytree(dist.location, dest)
                     else:
                         shutil.copy2(dist.location, dest)
 
-        # Create buildout script
-        ws = pkg_resources.WorkingSet(entries)
+        # Recreate a working set with the potentially-new paths after copying.
+        # We keep the eggs dists first since we know their locations contain a
+        # single dist. We add the other dists manually to avoid activating any
+        # unneded dists at the same location, and we can because these are the
+        # same dists as before as they were not copied.
+        ws = pkg_resources.WorkingSet(egg_entries)
+        for dist in link_dists:
+            ws.add(dist)
         ws.require('zc.buildout')
-        options = self['buildout']
-        buildout_dir = options['directory']
-        eggs_dir = options['eggs-directory']
-        develop_eggs_dir = options['develop-eggs-directory']
-        ws = zc.buildout.easy_install.sort_working_set(
-                ws,
-                buildout_dir=buildout_dir,
-                eggs_dir=eggs_dir,
-                develop_eggs_dir=develop_eggs_dir
-                )
+
+        # Create buildout script
         zc.buildout.easy_install.scripts(
             ['zc.buildout'], ws, sys.executable,
             options['bin-directory'],