Fix hierarchy of directories to look for loaders and modules

This fixes two longstanding problems.

First that starters had to ship with modules/utilities that Gatsby
already included and second that installing a starter with NPM 2 often
has problems.

I did some more research into this and realized the problem is that we
don't tell Gatsby to look in `/node_modules/gatsby/node_modules` to look
for modules and loaders. This means the starter also has to install them
(especially with NPM 2 which doesn't put dependencies of dependencies at
top-level of node_modules like NPM 3 does).

By telling Webpack to look in Gatsby's node_modules directory as well we
should be able to elimintate extra dependencies from starters as well as
fix intermittent NPM 2 problems.

lib/utils/webpack.config.js

@@ -162,13 +162,16 @@ module.exports = (program, directory, suppliedStage, webpackPort = 1500, routes
         '.toml',
         '.yaml',
       ],
+      // Hierarchy of directories for Webpack to look for module.
+      // First is the site directory.
+      // Then in the special directory of isomorphic modules Gatsby ships with.
+      // Then the site's node_modules directory
+      // and last the Gatsby node_modules directory.
       root: [
         directory,
         path.resolve(__dirname, '..', 'isomorphic'),
-      ],
-      modulesDirectories: [
-        `${directory}/node_modules`,
-        'node_modules',
+        path.resolve(directory, 'node_modules'),
+        path.resolve(directory, 'node_modules/gatsby/node_modules'),
       ],
     }
   }
@@ -430,12 +433,16 @@ module.exports = (program, directory, suppliedStage, webpackPort = 1500, routes
     devtool: devtool(),
     output: output(),
     resolveLoader: {
+      // Hierarchy of directories for Webpack to look for loaders.
+      // First is the /loaders/ directory in the site.
+      // Then in the special directory of loaders Gatsby ships with.
+      // Then the site's node_modules directory
+      // and last the Gatsby node_modules directory.
       root: [
         path.resolve(directory, 'loaders'),
         path.resolve(__dirname, '..', 'loaders'),
-      ],
-      modulesDirectories: [
-        'node_modules',
+        path.resolve(directory, 'node_modules'),
+        path.resolve(directory, 'node_modules/gatsby/node_modules'),
       ],
     },
     plugins: plugins(),