diff --git a/packages/babel-core/src/config/build-config-chain.js b/packages/babel-core/src/config/build-config-chain.js
index ec55737bbd..78e97794cf 100644
--- a/packages/babel-core/src/config/build-config-chain.js
+++ b/packages/babel-core/src/config/build-config-chain.js
@@ -18,12 +18,20 @@ type ConfigItem = {
   alias: string,
 };
 
-type ConfigRaw = {
-  type: "options" | "arguments",
-  options: {},
-  alias: string,
-  dirname: string,
-};
+type ConfigPart =
+  | {
+      part: "config",
+      config: ConfigItem,
+      ignore: ?Array<mixed>,
+      only: ?Array<mixed>,
+      activeEnv: string | null,
+    }
+  | {
+      part: "extends",
+      path: string,
+      dirname: string,
+      activeEnv: string | null,
+    };
 
 export default function buildConfigChain(opts: {}): Array<ConfigItem> | null {
   if (typeof opts.filename !== "string" && opts.filename != null) {
@@ -160,7 +168,7 @@ function flattenArgumentsOptionsParts(
   if (opts.extends != null) {
     raw.push(
       ...flattenOptionsParts(
-        buildArgumentsRawConfig({ extends: opts.extends }, dirname),
+        buildArgumentsItem({ extends: opts.extends }, dirname),
       ),
     );
   }
@@ -176,7 +184,7 @@ const flattenArgumentsEnvOptionsParts = makeWeakCache((env: {}) => {
   const options = { env };
 
   return makeStrongCache((dirname: string) =>
-    flattenOptionsPartsLookup(buildArgumentsRawConfig(options, dirname)),
+    flattenOptionsPartsLookup(buildArgumentsItem(options, dirname)),
   );
 });
 
@@ -189,7 +197,7 @@ const flattenArgumentsPluginsOptionsParts = makeWeakCache(
     const options = { plugins };
 
     return makeStrongCache((dirname: string) =>
-      flattenOptionsParts(buildArgumentsRawConfig(options, dirname)),
+      flattenOptionsParts(buildArgumentsItem(options, dirname)),
     );
   },
 );
@@ -207,12 +215,12 @@ const flattenArgumentsPresetsOptionsParts = makeWeakCache(
       const options = { presets, passPerPreset };
 
       return makeStrongCache((dirname: string) =>
-        flattenOptionsParts(buildArgumentsRawConfig(options, dirname)),
+        flattenOptionsParts(buildArgumentsItem(options, dirname)),
       );
     }),
 );
 
-function buildArgumentsRawConfig(options: {}, dirname: string): ConfigRaw {
+function buildArgumentsItem(options: {}, dirname: string): ConfigItem {
   return {
     type: "arguments",
     options,
@@ -240,7 +248,7 @@ const flattenFileOptionsParts = makeWeakCache((file: ConfigFile) => {
  * the environment passed as the first argument.
  */
 function flattenOptionsPartsLookup(
-  config: ConfigRaw,
+  config: ConfigItem,
 ): (string | null) => Array<ConfigPart> {
   const parts = flattenOptionsParts(config);
 
@@ -262,30 +270,15 @@ function flattenOptionsPartsLookup(
   return envKey => lookup.get(envKey) || def;
 }
 
-type ConfigPart =
-  | {
-      part: "config",
-      config: ConfigItem,
-      ignore: ?Array<mixed>,
-      only: ?Array<mixed>,
-      activeEnv: string | null,
-    }
-  | {
-      part: "extends",
-      path: string,
-      dirname: string,
-      activeEnv: string | null,
-    };
-
 /**
  * Given a generic config object, flatten it into its various parts so that
  * then can be cached and processed later.
  */
 function flattenOptionsParts(
-  rawConfig: ConfigRaw,
+  config: ConfigItem,
   activeEnv: string | null = null,
 ): Array<ConfigPart> {
-  const { type, options: rawOpts, alias, dirname } = rawConfig;
+  const { type, options: rawOpts, alias, dirname } = config;
 
   if (rawOpts.ignore != null && !Array.isArray(rawOpts.ignore)) {
     throw new Error(
@@ -340,18 +333,9 @@ function flattenOptionsParts(
     }
   });
 
-  const options = Object.assign({}, rawOpts);
-  delete options.env;
-  delete options.extends;
-
   parts.push({
     part: "config",
-    config: {
-      type,
-      options,
-      alias,
-      dirname,
-    },
+    config,
     ignore,
     only,
     activeEnv,
diff --git a/packages/babel-core/src/config/option-manager.js b/packages/babel-core/src/config/option-manager.js
index a5596f0c50..ae63a9ba92 100644
--- a/packages/babel-core/src/config/option-manager.js
+++ b/packages/babel-core/src/config/option-manager.js
@@ -137,7 +137,13 @@ class OptionManager {
       pass.unshift(...plugins);
     }
 
-    merge(this.options, result.options);
+    const options = Object.assign({}, result.options);
+    delete options.extends;
+    delete options.env;
+    delete options.plugins;
+    delete options.presets;
+
+    merge(this.options, options);
   }
 
   init(opts: {}) {
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index 1ab0ece980..e66d88d6cf 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -530,31 +530,31 @@ describe("api", function() {
     it("default", function() {
       const result = babel.transform("foo;", {
         env: {
-          development: { code: false },
+          development: { comments: false },
         },
       });
 
-      assert.equal(result.code, undefined);
+      assert.equal(result.options.comments, false);
     });
 
     it("BABEL_ENV", function() {
       process.env.BABEL_ENV = "foo";
       const result = babel.transform("foo;", {
         env: {
-          foo: { code: false },
+          foo: { comments: false },
         },
       });
-      assert.equal(result.code, undefined);
+      assert.equal(result.options.comments, false);
     });
 
     it("NODE_ENV", function() {
       process.env.NODE_ENV = "foo";
       const result = babel.transform("foo;", {
         env: {
-          foo: { code: false },
+          foo: { comments: false },
         },
       });
-      assert.equal(result.code, undefined);
+      assert.equal(result.options.comments, false);
     });
   });
 
diff --git a/packages/babel-core/test/config-chain.js b/packages/babel-core/test/config-chain.js
index 23c8d95a57..e004a8aaa2 100644
--- a/packages/babel-core/test/config-chain.js
+++ b/packages/babel-core/test/config-chain.js
@@ -72,7 +72,6 @@ describe("buildConfigChain", function() {
             ],
           },
           alias: "base",
-          loc: "base",
           dirname: base(),
         },
       ];
@@ -117,7 +116,6 @@ describe("buildConfigChain", function() {
             ],
           },
           alias: "base",
-          loc: "base",
           dirname: base(),
         },
       ];
@@ -379,16 +377,15 @@ describe("buildConfigChain", function() {
           plugins: ["extended"],
         },
         alias: fixture("extended.babelrc.json"),
-        loc: fixture("extended.babelrc.json"),
         dirname: fixture(),
       },
       {
         type: "options",
         options: {
+          extends: "./extended.babelrc.json",
           plugins: ["root"],
         },
         alias: fixture(".babelrc"),
-        loc: fixture(".babelrc"),
         dirname: fixture(),
       },
       {
@@ -397,7 +394,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -406,7 +402,6 @@ describe("buildConfigChain", function() {
           filename: fixture("dir1", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -426,7 +421,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -435,7 +429,6 @@ describe("buildConfigChain", function() {
           plugins: ["dir2"],
         },
         alias: fixture("dir2", ".babelrc"),
-        loc: fixture("dir2", ".babelrc"),
         dirname: fixture("dir2"),
       },
       {
@@ -444,7 +437,6 @@ describe("buildConfigChain", function() {
           filename: fixture("dir2", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -464,16 +456,15 @@ describe("buildConfigChain", function() {
           plugins: ["extended"],
         },
         alias: fixture("extended.babelrc.json"),
-        loc: fixture("extended.babelrc.json"),
         dirname: fixture(),
       },
       {
         type: "options",
         options: {
+          extends: "./extended.babelrc.json",
           plugins: ["root"],
         },
         alias: fixture(".babelrc"),
-        loc: fixture(".babelrc"),
         dirname: fixture(),
       },
       {
@@ -482,7 +473,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -491,7 +481,6 @@ describe("buildConfigChain", function() {
           filename: fixture("dir3", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -511,16 +500,22 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
         type: "options",
         options: {
+          env: {
+            bar: {
+              plugins: ["env-bar"],
+            },
+            foo: {
+              plugins: ["env-foo"],
+            },
+          },
           plugins: ["env-base"],
         },
         alias: fixture("env", ".babelrc"),
-        loc: fixture("env", ".babelrc"),
         dirname: fixture("env"),
       },
       {
@@ -529,7 +524,6 @@ describe("buildConfigChain", function() {
           filename: fixture("env", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -551,16 +545,22 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
         type: "options",
         options: {
+          env: {
+            bar: {
+              plugins: ["env-bar"],
+            },
+            foo: {
+              plugins: ["env-foo"],
+            },
+          },
           plugins: ["env-base"],
         },
         alias: fixture("env", ".babelrc"),
-        loc: fixture("env", ".babelrc"),
         dirname: fixture("env"),
       },
       {
@@ -569,7 +569,6 @@ describe("buildConfigChain", function() {
           plugins: ["env-foo"],
         },
         alias: fixture("env", ".babelrc.env.foo"),
-        loc: fixture("env", ".babelrc.env.foo"),
         dirname: fixture("env"),
       },
       {
@@ -578,7 +577,6 @@ describe("buildConfigChain", function() {
           filename: fixture("env", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -601,16 +599,22 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
         type: "options",
         options: {
+          env: {
+            bar: {
+              plugins: ["env-bar"],
+            },
+            foo: {
+              plugins: ["env-foo"],
+            },
+          },
           plugins: ["env-base"],
         },
         alias: fixture("env", ".babelrc"),
-        loc: fixture("env", ".babelrc"),
         dirname: fixture("env"),
       },
       {
@@ -619,7 +623,6 @@ describe("buildConfigChain", function() {
           plugins: ["env-bar"],
         },
         alias: fixture("env", ".babelrc.env.bar"),
-        loc: fixture("env", ".babelrc.env.bar"),
         dirname: fixture("env"),
       },
       {
@@ -628,7 +631,6 @@ describe("buildConfigChain", function() {
           filename: fixture("env", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -650,7 +652,6 @@ describe("buildConfigChain", function() {
           plugins: ["pkg-plugin"],
         },
         alias: fixture("pkg", "package.json"),
-        loc: fixture("pkg", "package.json"),
         dirname: fixture("pkg"),
       },
       {
@@ -659,7 +660,6 @@ describe("buildConfigChain", function() {
           ignore: ["pkg-ignore"],
         },
         alias: fixture("pkg", ".babelignore"),
-        loc: fixture("pkg", ".babelignore"),
         dirname: fixture("pkg"),
       },
       {
@@ -668,7 +668,6 @@ describe("buildConfigChain", function() {
           filename: fixture("pkg", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -688,7 +687,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -697,7 +695,6 @@ describe("buildConfigChain", function() {
           plugins: ["foo", "bar"],
         },
         alias: fixture("js-config", ".babelrc.js"),
-        loc: fixture("js-config", ".babelrc.js"),
         dirname: fixture("js-config"),
       },
       {
@@ -706,7 +703,6 @@ describe("buildConfigChain", function() {
           filename: fixture("js-config", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -726,7 +722,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -735,7 +730,6 @@ describe("buildConfigChain", function() {
           compact: true,
         },
         alias: fixture("js-config-function", ".babelrc.js"),
-        loc: fixture("js-config-function", ".babelrc.js"),
         dirname: fixture("js-config-function"),
       },
       {
@@ -744,7 +738,6 @@ describe("buildConfigChain", function() {
           filename: fixture("js-config-function", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -764,7 +757,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -773,7 +765,6 @@ describe("buildConfigChain", function() {
           plugins: ["foo", "bar"],
         },
         alias: fixture("js-config-default", ".babelrc.js"),
-        loc: fixture("js-config-default", ".babelrc.js"),
         dirname: fixture("js-config-default"),
       },
       {
@@ -782,7 +773,6 @@ describe("buildConfigChain", function() {
           filename: fixture("js-config-default", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -801,7 +791,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -810,16 +799,15 @@ describe("buildConfigChain", function() {
           plugins: ["extended"],
         },
         alias: fixture("extended.babelrc.json"),
-        loc: fixture("extended.babelrc.json"),
         dirname: fixture(),
       },
       {
         type: "options",
         options: {
+          extends: "../extended.babelrc.json",
           plugins: ["foo", "bar"],
         },
         alias: fixture("js-config-extended", ".babelrc.js"),
-        loc: fixture("js-config-extended", ".babelrc.js"),
         dirname: fixture("js-config-extended"),
       },
       {
@@ -828,7 +816,6 @@ describe("buildConfigChain", function() {
           filename: fixture("js-config-extended", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -851,7 +838,6 @@ describe("buildConfigChain", function() {
             ignore: ["root-ignore"],
           },
           alias: fixture(".babelignore"),
-          loc: fixture(".babelignore"),
           dirname: fixture(),
         },
         {
@@ -860,7 +846,6 @@ describe("buildConfigChain", function() {
             plugins: ["json"],
           },
           alias: fixture("json-pkg-config-no-babel", ".babelrc"),
-          loc: fixture("json-pkg-config-no-babel", ".babelrc"),
           dirname: fixture("json-pkg-config-no-babel"),
         },
         {
@@ -869,7 +854,6 @@ describe("buildConfigChain", function() {
             filename: fixture("json-pkg-config-no-babel", "src.js"),
           },
           alias: "base",
-          loc: "base",
           dirname: base(),
         },
       ];
@@ -890,7 +874,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -899,7 +882,6 @@ describe("buildConfigChain", function() {
           ignore: ["*", "!src.js"],
         },
         alias: fixture("ignore-negate", ".babelrc"),
-        loc: fixture("ignore-negate", ".babelrc"),
         dirname: fixture("ignore-negate"),
       },
       {
@@ -908,7 +890,6 @@ describe("buildConfigChain", function() {
           filename: fixture("ignore-negate", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];
@@ -934,7 +915,6 @@ describe("buildConfigChain", function() {
           ignore: ["root-ignore"],
         },
         alias: fixture(".babelignore"),
-        loc: fixture(".babelignore"),
         dirname: fixture(),
       },
       {
@@ -943,7 +923,6 @@ describe("buildConfigChain", function() {
           ignore: ["*", "!folder"],
         },
         alias: fixture("ignore-negate-folder", ".babelrc"),
-        loc: fixture("ignore-negate-folder", ".babelrc"),
         dirname: fixture("ignore-negate-folder"),
       },
       {
@@ -952,7 +931,6 @@ describe("buildConfigChain", function() {
           filename: fixture("ignore-negate-folder", "folder", "src.js"),
         },
         alias: "base",
-        loc: "base",
         dirname: base(),
       },
     ];