[feat] Warn when bootstrap finds dists in site-packages

And avoid creating a .egg-link pointing to site-packages.

src/zc/buildout/buildout.py

@@ -762,10 +762,15 @@ class Buildout(DictMixin):
         # nothing will be installed, but then we'll copy them to
         # the local eggs or develop-eggs folder just after this.
 
-        # 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.
+        # XXX Note: except if the current modules are not eggs. In particular,
+        # this concerns .dist-info packages installed by pip in site-packages
+        # or elsewhere: setuptools does not distinguish dists installed by pip
+        # from actual develop dists. This may lead to the creation of .egg-link
+        # files in ./develop-eggs linking to the original location.
+        # A special-case exception is made when the location is site-packages
+        # to avoid putting links to site-packages in ./develop-eggs. This is
+        # merely a mitigation and does not preclude other shared locations
+        # being linked in ./develop-eggs.
 
         # Sort the working set to keep entries with single dists first.
         options = self['buildout']
@@ -786,11 +791,25 @@ class Buildout(DictMixin):
         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)
-                link_dists.append(dist)
+                if dist.location == zc.buildout.easy_install.python_lib:
+                    # Special-case exception for site-packages
+                    self._logger.warning(
+                        "Distribution %s was found in sites-packages (%s). "
+                        "Avoiding creating a link in develop-eggs-directory.\n"
+                        "Consider using 'buildout:extra-paths=' to install it "
+                        "from scratch in isolation directly in eggs-directory")
+                    # XXX: TODO: Ideally we should be able to distinguish
+                    # .dist-info dists from develop dists, and support bundling
+                    # .dist-info packages into individual '.dist' bundles that
+                    # could be put in ./eggs, with support in buildout for
+                    # using such distribution.
+                else:
+                    dest = os.path.join(
+                      self['buildout']['develop-eggs-directory'],
+                      dist.key + '.egg-link')
+                    with open(dest, 'w') as fh:
+                        fh.write(dist.location)
+                    link_dists.append(dist)
             else:
                 dest = os.path.join(self['buildout']['eggs-directory'],
                                     os.path.basename(dist.location))