diff --git a/package.json b/package.json
index b4ebcee5a0..673ada54f5 100644
--- a/package.json
+++ b/package.json
@@ -27,7 +27,7 @@
     "eslint": "^3.9.0",
     "eslint-config-babel": "^6.0.0",
     "eslint-plugin-flowtype": "^2.20.0",
-    "flow-bin": "^0.34.0",
+    "flow-bin": "^0.41.0",
     "gulp": "^3.9.0",
     "gulp-babel": "^6.0.0",
     "gulp-newer": "^1.0.0",
diff --git a/packages/babel-core/src/transformation/file/options/build-config-chain.js b/packages/babel-core/src/config/build-config-chain.js
similarity index 97%
rename from packages/babel-core/src/transformation/file/options/build-config-chain.js
rename to packages/babel-core/src/config/build-config-chain.js
index df05a06443..a8659f0960 100644
--- a/packages/babel-core/src/transformation/file/options/build-config-chain.js
+++ b/packages/babel-core/src/config/build-config-chain.js
@@ -1,5 +1,5 @@
-import * as babel from "../../../index";
-import resolve from "../../../helpers/resolve";
+import * as babel from "../index";
+import resolve from "./helpers/resolve";
 import json5 from "json5";
 import path from "path";
 import fs from "fs";
@@ -28,6 +28,7 @@ export default function buildConfigChain(opts: Object = {}) {
 
   try {
     builder.mergeConfig({
+      type: "arguments",
       options: opts,
       alias: "base",
       dirname: process.cwd(),
@@ -185,6 +186,7 @@ class ConfigChainBuilder {
 
     if (lines.length) {
       this.mergeConfig({
+        type: "options",
         options: { ignore: lines },
         alias: loc,
         dirname: path.dirname(loc),
@@ -231,6 +233,7 @@ class ConfigChainBuilder {
     }
 
     this.mergeConfig({
+      type: "options",
       options,
       alias: loc,
       dirname: path.dirname(loc),
@@ -240,6 +243,7 @@ class ConfigChainBuilder {
   }
 
   mergeConfig({
+    type,
     options,
     alias,
     loc,
@@ -266,6 +270,7 @@ class ConfigChainBuilder {
       delete options.env;
 
       this.mergeConfig({
+        type,
         options: envOpts,
         alias: `${alias}.env.${envKey}`,
         dirname: dirname,
@@ -273,6 +278,7 @@ class ConfigChainBuilder {
     }
 
     this.configs.push({
+      type,
       options,
       alias,
       loc,
diff --git a/packages/babel-core/src/helpers/environment.js b/packages/babel-core/src/config/helpers/environment.js
similarity index 100%
rename from packages/babel-core/src/helpers/environment.js
rename to packages/babel-core/src/config/helpers/environment.js
diff --git a/packages/babel-core/src/helpers/get-possible-plugin-names.js b/packages/babel-core/src/config/helpers/get-possible-plugin-names.js
similarity index 100%
rename from packages/babel-core/src/helpers/get-possible-plugin-names.js
rename to packages/babel-core/src/config/helpers/get-possible-plugin-names.js
diff --git a/packages/babel-core/src/helpers/get-possible-preset-names.js b/packages/babel-core/src/config/helpers/get-possible-preset-names.js
similarity index 100%
rename from packages/babel-core/src/helpers/get-possible-preset-names.js
rename to packages/babel-core/src/config/helpers/get-possible-preset-names.js
diff --git a/packages/babel-core/src/helpers/merge.js b/packages/babel-core/src/config/helpers/merge.js
similarity index 100%
rename from packages/babel-core/src/helpers/merge.js
rename to packages/babel-core/src/config/helpers/merge.js
diff --git a/packages/babel-core/src/helpers/resolve-from-possible-names.js b/packages/babel-core/src/config/helpers/resolve-from-possible-names.js
similarity index 100%
rename from packages/babel-core/src/helpers/resolve-from-possible-names.js
rename to packages/babel-core/src/config/helpers/resolve-from-possible-names.js
diff --git a/packages/babel-core/src/helpers/resolve-plugin.js b/packages/babel-core/src/config/helpers/resolve-plugin.js
similarity index 100%
rename from packages/babel-core/src/helpers/resolve-plugin.js
rename to packages/babel-core/src/config/helpers/resolve-plugin.js
diff --git a/packages/babel-core/src/helpers/resolve-preset.js b/packages/babel-core/src/config/helpers/resolve-preset.js
similarity index 100%
rename from packages/babel-core/src/helpers/resolve-preset.js
rename to packages/babel-core/src/config/helpers/resolve-preset.js
diff --git a/packages/babel-core/src/helpers/resolve.js b/packages/babel-core/src/config/helpers/resolve.js
similarity index 100%
rename from packages/babel-core/src/helpers/resolve.js
rename to packages/babel-core/src/config/helpers/resolve.js
diff --git a/packages/babel-core/src/config/index.js b/packages/babel-core/src/config/index.js
new file mode 100644
index 0000000000..3c8f49a157
--- /dev/null
+++ b/packages/babel-core/src/config/index.js
@@ -0,0 +1,30 @@
+import type Plugin from "./plugin";
+import OptionManager from "./option-manager";
+
+export type ResolvedConfig = {
+  options: Object,
+  passes: Array<Array<Plugin>>,
+};
+
+/**
+ * Standard API for loading Babel configuration data. Not for public consumption.
+ */
+export default function loadConfig(opts: Object): ResolvedConfig|null {
+  const mergedOpts = new OptionManager().init(opts);
+  if (!mergedOpts) return null;
+
+  let passes = [];
+  if (mergedOpts.plugins) {
+    passes.push(mergedOpts.plugins);
+  }
+
+  // With "passPerPreset" enabled there may still be presets in the options.
+  if (mergedOpts.presets) {
+    passes = passes.concat(mergedOpts.presets.map((preset) => preset.plugins).filter(Boolean));
+  }
+
+  return {
+    options: mergedOpts,
+    passes,
+  };
+}
diff --git a/packages/babel-core/src/transformation/file/options/option-manager.js b/packages/babel-core/src/config/option-manager.js
similarity index 77%
rename from packages/babel-core/src/transformation/file/options/option-manager.js
rename to packages/babel-core/src/config/option-manager.js
index df43555c5f..cb501f00b8 100644
--- a/packages/babel-core/src/transformation/file/options/option-manager.js
+++ b/packages/babel-core/src/config/option-manager.js
@@ -1,15 +1,15 @@
-import * as context from "../../../index";
-import Plugin from "../../plugin";
+import * as context from "../index";
+import Plugin from "./plugin";
 import * as messages from "babel-messages";
-import resolvePlugin from "../../../helpers/resolve-plugin";
-import resolvePreset from "../../../helpers/resolve-preset";
+import resolve from "./helpers/resolve";
+import resolvePlugin from "./helpers/resolve-plugin";
+import resolvePreset from "./helpers/resolve-preset";
 import defaults from "lodash/defaults";
 import cloneDeepWith from "lodash/cloneDeepWith";
-import merge from "../../../helpers/merge";
+import merge from "./helpers/merge";
 import removed from "./removed";
 import buildConfigChain from "./build-config-chain";
 import path from "path";
-import * as util from "../../../util";
 
 type PluginObject = {
   pre?: Function;
@@ -25,6 +25,7 @@ type PluginObject = {
 };
 
 type MergeOptions = {
+  type: "arguments"|"options"|"preset",
   options?: Object,
   extending?: Object,
   alias: string,
@@ -188,6 +189,7 @@ export default class OptionManager {
    */
 
   mergeOptions({
+    type,
     options: rawOpts,
     extending: extendingOpts,
     alias,
@@ -213,6 +215,23 @@ export default class OptionManager {
     dirname = dirname || process.cwd();
     loc = loc || alias;
 
+    if (type !== "arguments") {
+      if (opts.filename !== undefined) {
+        throw new Error(`${alias}.filename is only allowed as a root argument`);
+      }
+
+      if (opts.babelrc !== undefined) {
+        throw new Error(`${alias}.babelrc is only allowed as a root argument`);
+      }
+    }
+
+    if (type === "preset") {
+      if (opts.only !== undefined) throw new Error(`${alias}.only is not supported in a preset`);
+      if (opts.ignore !== undefined) throw new Error(`${alias}.ignore is not supported in a preset`);
+      if (opts.extends !== undefined) throw new Error(`${alias}.extends is not supported in a preset`);
+      if (opts.env !== undefined) throw new Error(`${alias}.env is not supported in a preset`);
+    }
+
     if (opts.sourceMap !== undefined) {
       if (opts.sourceMaps !== undefined) {
         throw new Error(`Both ${alias}.sourceMap and .sourceMaps have been set`);
@@ -236,6 +255,26 @@ export default class OptionManager {
       }
     }
 
+    if (opts.parserOpts && typeof opts.parserOpts.parser === "string") {
+      const parser = resolve(opts.parserOpts.parser, dirname);
+      if (parser) {
+        opts.parserOpts.parser = require(parser).parse;
+      } else {
+        throw new Error(`Couldn't find parser ${opts.parserOpts.parser} with "parse" method ` +
+          `relative to directory ${dirname}`);
+      }
+    }
+
+    if (opts.generatorOpts && typeof opts.generatorOpts.generator === "string") {
+      const generator = resolve(opts.generatorOpts.generator, dirname);
+      if (generator) {
+        opts.generatorOpts.generator = require(generator).print;
+      } else {
+        throw new Error(`Couldn't find generator ${opts.generatorOpts.generator} with "print" method ` +
+          `relative to directory ${dirname}`);
+      }
+    }
+
     // resolve plugins
     if (opts.plugins) {
       if (!Array.isArray(rawOpts.plugins)) throw new Error(`${alias}.plugins should be an array`);
@@ -247,23 +286,22 @@ export default class OptionManager {
     if (opts.presets) {
       if (!Array.isArray(rawOpts.presets)) throw new Error(`${alias}.presets should be an array`);
 
-      // If we're in the "pass per preset" mode, we resolve the presets
-      // and keep them for further execution to calculate the options.
-      if (opts.passPerPreset) {
-        opts.presets = this.resolvePresets(opts.presets, dirname, (preset, presetLoc) => {
-          this.mergeOptions({
-            options: preset,
-            extending: preset,
-            alias: presetLoc,
-            loc: presetLoc,
-            dirname: dirname,
-          });
+      opts.presets = this.resolvePresets(opts.presets, dirname, (preset, presetLoc) => {
+        this.mergeOptions({
+          type: "preset",
+          options: preset,
+
+          // For `passPerPreset` we merge child options back into the preset object instead of the root.
+          extending: opts.passPerPreset ? preset : null,
+          alias: presetLoc,
+          loc: presetLoc,
+          dirname: dirname,
         });
-      } else {
-        // Otherwise, just merge presets options into the main options.
-        this.mergePresets(opts.presets, dirname);
-        delete opts.presets;
-      }
+      });
+
+      // If not passPerPreset, the plugins have all been merged into the parent config so the presets
+      // list is not needed.
+      if (!opts.passPerPreset) delete opts.presets;
     }
 
     // Merge them into current extending options in case of top-level
@@ -276,21 +314,6 @@ export default class OptionManager {
     }
   }
 
-  /**
-   * Merges all presets into the main options in case we are not in the
-   * "pass per preset" mode. Otherwise, options are calculated per preset.
-   */
-  mergePresets(presets: Array<string | Object>, dirname: string) {
-    this.resolvePresets(presets, dirname, (presetOpts, presetLoc) => {
-      this.mergeOptions({
-        options: presetOpts,
-        alias: presetLoc,
-        loc: presetLoc,
-        dirname: path.dirname(presetLoc || ""),
-      });
-    });
-  }
-
   /**
    * Resolves presets options which can be either direct object data,
    * or a module name to require.
@@ -370,7 +393,12 @@ export default class OptionManager {
         this.mergeOptions(config);
       }
     } catch (e) {
-      e.message = util.message(opts, e.message);
+      // There are a few case where thrown errors will try to annotate themselves multiple times, so
+      // to keep things simple we just bail out if re-wrapping the message.
+      if (!/^\[BABEL\]/.test(e.message)) {
+        e.message = `[BABEL] ${opts.filename || "unknown"}: ${e.message}`;
+      }
+
       throw e;
     }
 
diff --git a/packages/babel-core/src/transformation/plugin.js b/packages/babel-core/src/config/plugin.js
similarity index 93%
rename from packages/babel-core/src/transformation/plugin.js
rename to packages/babel-core/src/config/plugin.js
index 75665c1552..fb637d7cee 100644
--- a/packages/babel-core/src/transformation/plugin.js
+++ b/packages/babel-core/src/config/plugin.js
@@ -1,15 +1,12 @@
-import OptionManager from "./file/options/option-manager";
+import OptionManager from "./option-manager";
 import * as messages from "babel-messages";
-import Store from "../store";
 import traverse from "babel-traverse";
 import clone from "lodash/clone";
 
 const GLOBAL_VISITOR_PROPS = ["enter", "exit"];
 
-export default class Plugin extends Store {
+export default class Plugin {
   constructor(plugin: Object, key?: string) {
-    super();
-
     this.initialized = false;
     this.raw = Object.assign({}, plugin);
     this.key = this.take("name") || key;
diff --git a/packages/babel-core/src/transformation/file/options/removed.js b/packages/babel-core/src/config/removed.js
similarity index 100%
rename from packages/babel-core/src/transformation/file/options/removed.js
rename to packages/babel-core/src/config/removed.js
diff --git a/packages/babel-core/src/helpers/normalize-ast.js b/packages/babel-core/src/helpers/normalize-ast.js
deleted file mode 100644
index d2c91cef91..0000000000
--- a/packages/babel-core/src/helpers/normalize-ast.js
+++ /dev/null
@@ -1,23 +0,0 @@
-import * as t from "babel-types";
-
-/**
- * Normalize an AST.
- *
- * - Wrap `Program` node with a `File` node.
- */
-
-export default function (
-  ast: Object,
-  comments?: Array<Object>,
-  tokens?: Array<Object>,
-) {
-  if (ast) {
-    if (ast.type === "Program") {
-      return t.file(ast, comments || [], tokens || []);
-    } else if (ast.type === "File") {
-      return ast;
-    }
-  }
-
-  throw new Error("Not a valid ast?");
-}
diff --git a/packages/babel-core/src/index.js b/packages/babel-core/src/index.js
index f3fa340eb5..75741c26be 100644
--- a/packages/babel-core/src/index.js
+++ b/packages/babel-core/src/index.js
@@ -1,17 +1,30 @@
 export File from "./transformation/file";
 export buildExternalHelpers from "./tools/build-external-helpers";
-export resolvePlugin from "./helpers/resolve-plugin";
-export resolvePreset from "./helpers/resolve-preset";
+export resolvePlugin from "./config/helpers/resolve-plugin";
+export resolvePreset from "./config/helpers/resolve-preset";
 
 export { version } from "../package";
-export { getEnv } from "./helpers/environment";
+export { getEnv } from "./config/helpers/environment";
 
 export * as messages from "babel-messages";
 export * as types from "babel-types";
 export traverse from "babel-traverse";
 export template from "babel-template";
 
-export OptionManager from "./transformation/file/options/option-manager";
+import loadConfig from "./config";
+
+export function loadOptions(opts): Object|null {
+  const config = loadConfig(opts);
+
+  return config ? config.options : null;
+}
+
+// For easier backward-compatibility, provide an API like the one we exposed in Babel 6.
+export class OptionManager {
+  init(opts) {
+    return loadOptions(opts);
+  }
+}
 
 export function Plugin(alias) {
   throw new Error(`The (${alias}) Babel 5 plugin is being run with Babel 6.`);
diff --git a/packages/babel-core/src/transformation/file/index.js b/packages/babel-core/src/transformation/file/index.js
index 9d5af49ff0..dc940b53de 100644
--- a/packages/babel-core/src/transformation/file/index.js
+++ b/packages/babel-core/src/transformation/file/index.js
@@ -9,23 +9,28 @@ import sourceMap from "source-map";
 import generate from "babel-generator";
 import codeFrame from "babel-code-frame";
 import traverse from "babel-traverse";
-import Store from "../../store";
+import Store from "../store";
 import { parse } from "babylon";
-import * as util from "../../util";
-import path from "path";
 import * as t from "babel-types";
+import buildDebug from "debug";
 
-import resolve from "../../helpers/resolve";
+import loadConfig, { type ResolvedConfig } from "../../config";
 
 import blockHoistPlugin from "../internal-plugins/block-hoist";
 import shadowFunctionsPlugin from "../internal-plugins/shadow-functions";
 
+const babelDebug = buildDebug("babel:file");
+
+export function debug(opts: Object, msg: string) {
+  babelDebug(`${opts.filename || "unknown"}: ${msg}`);
+}
+
 const shebangRegex = /^#!.*/;
 
-const INTERNAL_PLUGINS = [
-  [blockHoistPlugin],
-  [shadowFunctionsPlugin],
-];
+const INTERNAL_PLUGINS = loadConfig({
+  babelrc: false,
+  plugins: [ blockHoistPlugin, shadowFunctionsPlugin ],
+}).passes[0];
 
 const errorVisitor = {
   enter(path, state) {
@@ -38,17 +43,11 @@ const errorVisitor = {
 };
 
 export default class File extends Store {
-  constructor(opts: Object = {}) {
+  constructor({ options, passes }: ResolvedConfig) {
     super();
 
-    let passes = [];
-    if (opts.plugins) passes.push(opts.plugins);
-
-    // With "passPerPreset" enabled there may still be presets in the options.
-    if (opts.presets) passes = passes.concat(opts.presets.map((preset) => preset.plugins).filter(Boolean));
-
     this.pluginPasses = passes;
-    this.opts = opts;
+    this.opts = options;
 
     this.parserOpts = {
       sourceType: this.opts.sourceType,
@@ -59,7 +58,7 @@ export default class File extends Store {
     for (const pluginPairs of passes) {
       for (const [ plugin ] of pluginPairs) {
         if (plugin.manipulateOptions) {
-          plugin.manipulateOptions(opts, this.parserOpts, this);
+          plugin.manipulateOptions(this.opts, this.parserOpts, this);
         }
       }
     }
@@ -340,18 +339,7 @@ export default class File extends Store {
       parserOpts = Object.assign({}, this.parserOpts, parserOpts);
 
       if (parserOpts.parser) {
-        if (typeof parserOpts.parser === "string") {
-          const dirname = path.dirname(this.opts.filename) || process.cwd();
-          const parser = resolve(parserOpts.parser, dirname);
-          if (parser) {
-            parseCode = require(parser).parse;
-          } else {
-            throw new Error(`Couldn't find parser ${parserOpts.parser} with "parse" method ` +
-              `relative to directory ${dirname}`);
-          }
-        } else {
-          parseCode = parserOpts.parser;
-        }
+        parseCode = parserOpts.parser;
 
         parserOpts.parser = {
           parse(source) {
@@ -361,9 +349,9 @@ export default class File extends Store {
       }
     }
 
-    util.debug(this.opts, "Parse start");
+    debug(this.opts, "Parse start");
     const ast = parseCode(code, parserOpts || this.parserOpts);
-    util.debug(this.opts, "Parse stop");
+    debug(this.opts, "Parse stop");
     return ast;
   }
 
@@ -381,31 +369,43 @@ export default class File extends Store {
   }
 
   addAst(ast) {
-    util.debug(this.opts, "Start set AST");
+    debug(this.opts, "Start set AST");
     this._addAst(ast);
-    util.debug(this.opts, "End set AST");
+    debug(this.opts, "End set AST");
   }
 
   transform(): BabelFileResult {
     for (const pluginPairs of this.pluginPasses) {
+      const passPairs = [];
       const passes = [];
       const visitors = [];
 
       for (const [ plugin, pluginOpts ] of pluginPairs.concat(INTERNAL_PLUGINS)) {
-        const pass = new PluginPass(this, plugin, pluginOpts);
+        const pass = new PluginPass(this, plugin.key, pluginOpts);
+
+        passPairs.push([ plugin, pass ]);
         passes.push(pass);
         visitors.push(plugin.visitor);
       }
 
-      this.call("pre", passes);
-      util.debug(this.opts, "Start transform traverse");
+      for (const [ plugin, pass ] of passPairs) {
+        const fn = plugin.pre;
+        if (fn) fn.call(pass, this);
+      }
+
+      debug(this.opts, "Start transform traverse");
 
       // merge all plugin visitors into a single visitor
       const visitor = traverse.visitors.merge(visitors, passes, this.opts.wrapPluginVisitorMethod);
       traverse(this.ast, visitor, this.scope);
 
-      util.debug(this.opts, "End transform traverse");
-      this.call("post", passes);
+      debug(this.opts, "End transform traverse");
+
+      for (const [ plugin, pass ] of passPairs) {
+        const fn = plugin.post;
+        if (fn) fn.call(pass, this);
+      }
+
     }
 
     return this.generate();
@@ -458,14 +458,6 @@ export default class File extends Store {
     this.addAst(ast);
   }
 
-  call(key: "pre" | "post", pluginPasses: Array<PluginPass>) {
-    for (const pass of pluginPasses) {
-      const plugin = pass.plugin;
-      const fn = plugin[key];
-      if (fn) fn.call(pass, this);
-    }
-  }
-
   parseInputSourceMap(code: string): string {
     const opts = this.opts;
 
@@ -523,27 +515,16 @@ export default class File extends Store {
     let gen = generate;
     if (opts.generatorOpts && opts.generatorOpts.generator) {
       gen = opts.generatorOpts.generator;
-
-      if (typeof gen === "string") {
-        const dirname = path.dirname(this.opts.filename) || process.cwd();
-        const generator = resolve(gen, dirname);
-        if (generator) {
-          gen = require(generator).print;
-        } else {
-          throw new Error(`Couldn't find generator ${gen} with "print" method relative ` +
-            `to directory ${dirname}`);
-        }
-      }
     }
 
-    util.debug(this.opts, "Generation start");
+    debug(this.opts, "Generation start");
 
     const _result = gen(ast, opts.generatorOpts ? Object.assign(opts, opts.generatorOpts) : opts,
       this.code);
     result.code = _result.code;
     result.map = _result.map;
 
-    util.debug(this.opts, "Generation end");
+    debug(this.opts, "Generation end");
 
     if (this.shebang) {
       // add back shebang
diff --git a/packages/babel-core/src/transformation/internal-plugins/block-hoist.js b/packages/babel-core/src/transformation/internal-plugins/block-hoist.js
index 35dee65312..4813b18d22 100644
--- a/packages/babel-core/src/transformation/internal-plugins/block-hoist.js
+++ b/packages/babel-core/src/transformation/internal-plugins/block-hoist.js
@@ -1,7 +1,6 @@
-import Plugin from "../plugin";
 import sortBy from "lodash/sortBy";
 
-export default new Plugin({
+export default {
   /**
    * [Please add a description.]
    *
@@ -39,4 +38,4 @@ export default new Plugin({
       },
     },
   },
-});
+};
diff --git a/packages/babel-core/src/transformation/internal-plugins/shadow-functions.js b/packages/babel-core/src/transformation/internal-plugins/shadow-functions.js
index ce50d21c01..45122a0a3f 100644
--- a/packages/babel-core/src/transformation/internal-plugins/shadow-functions.js
+++ b/packages/babel-core/src/transformation/internal-plugins/shadow-functions.js
@@ -1,4 +1,3 @@
-import Plugin from "../plugin";
 import * as t from "babel-types";
 
 const SUPER_THIS_BOUND = Symbol("super this bound");
@@ -15,7 +14,7 @@ const superVisitor = {
   },
 };
 
-export default new Plugin({
+export default {
   name: "internal.shadowFunctions",
 
   visitor: {
@@ -29,7 +28,7 @@ export default new Plugin({
       }
     },
   },
-});
+};
 
 function shouldShadow(path, shadowPath) {
   if (path.is("_forceShadow")) {
diff --git a/packages/babel-core/src/transformation/pipeline.js b/packages/babel-core/src/transformation/pipeline.js
index 9bf718a47e..24066e9b1c 100644
--- a/packages/babel-core/src/transformation/pipeline.js
+++ b/packages/babel-core/src/transformation/pipeline.js
@@ -1,25 +1,24 @@
 /* global BabelFileResult, BabelFileMetadata */
 import fs from "fs";
 
-import normalizeAst from "../helpers/normalize-ast";
-import Plugin from "./plugin";
+import * as t from "babel-types";
 import File from "./file";
-import OptionManager from "./file/options/option-manager";
+import loadConfig from "../config";
 
 export function analyse(code: string, opts: Object = {}, visitor?: Object): ?BabelFileMetadata {
   opts.code = false;
   if (visitor) {
     opts.plugins = opts.plugins || [];
-    opts.plugins.push(new Plugin({ visitor }));
+    opts.plugins.push({ visitor });
   }
   return transform(code, opts).metadata;
 }
 
 export function transform(code: string, opts?: Object): BabelFileResult {
-  opts = new OptionManager().init(opts);
-  if (opts === null) return null;
+  const config = loadConfig(opts);
+  if (config === null) return null;
 
-  const file = new File(opts);
+  const file = new File(config);
   return file.wrap(code, function () {
     file.addCode(code);
     file.parseCode(code);
@@ -28,12 +27,16 @@ export function transform(code: string, opts?: Object): BabelFileResult {
 }
 
 export function transformFromAst(ast: Object, code: string, opts: Object): BabelFileResult {
-  opts = new OptionManager().init(opts);
-  if (opts === null) return null;
+  const config = loadConfig(opts);
+  if (config === null) return null;
 
-  ast = normalizeAst(ast);
+  if (ast && ast.type === "Program") {
+    return t.file(ast, [], []);
+  } else if (!ast || ast.type !== "File") {
+    throw new Error("Not a valid ast?");
+  }
 
-  const file = new File(opts);
+  const file = new File(config);
   return file.wrap(code, function () {
     file.addCode(code);
     file.addAst(ast);
@@ -48,15 +51,15 @@ export function transformFile(filename: string, opts?: Object, callback: Functio
   }
 
   opts.filename = filename;
-  opts = new OptionManager().init(opts);
-  if (opts === null) return callback(null, null);
+  const config = loadConfig(opts);
+  if (config === null) return callback(null, null);
 
   fs.readFile(filename, function (err, code) {
     let result;
 
     if (!err) {
       try {
-        const file = new File(opts);
+        const file = new File(config);
         result = file.wrap(code, function () {
           file.addCode(code);
           file.parseCode(code);
@@ -77,11 +80,11 @@ export function transformFile(filename: string, opts?: Object, callback: Functio
 
 export function transformFileSync(filename: string, opts?: Object = {}): string {
   opts.filename = filename;
-  opts = new OptionManager().init(opts);
-  if (opts === null) return null;
+  const config = loadConfig(opts);
+  if (config === null) return null;
 
   const code = fs.readFileSync(filename, "utf8");
-  const file = new File(opts);
+  const file = new File(config);
 
   return file.wrap(code, function () {
     file.addCode(code);
diff --git a/packages/babel-core/src/transformation/plugin-pass.js b/packages/babel-core/src/transformation/plugin-pass.js
index 5e7ddb205d..c0a6626cf5 100644
--- a/packages/babel-core/src/transformation/plugin-pass.js
+++ b/packages/babel-core/src/transformation/plugin-pass.js
@@ -1,18 +1,16 @@
-import type Plugin from "./plugin";
-import Store from "../store";
+import Store from "./store";
 import File from "./file";
 
 export default class PluginPass extends Store {
-  constructor(file: File, plugin: Plugin, options: Object = {}) {
+  constructor(file: File, key: string, options: Object = {}) {
     super();
-    this.plugin = plugin;
-    this.key = plugin.key;
+
+    this.key = key;
     this.file = file;
     this.opts = options;
   }
 
   key: string;
-  plugin: Plugin;
   file: File;
   opts: Object;
 
diff --git a/packages/babel-core/src/store.js b/packages/babel-core/src/transformation/store.js
similarity index 100%
rename from packages/babel-core/src/store.js
rename to packages/babel-core/src/transformation/store.js
diff --git a/packages/babel-core/src/util.js b/packages/babel-core/src/util.js
deleted file mode 100644
index 3caa4be75e..0000000000
--- a/packages/babel-core/src/util.js
+++ /dev/null
@@ -1,17 +0,0 @@
-import buildDebug from "debug";
-
-export { inherits, inspect } from "util";
-
-const debugBabel = buildDebug("babel");
-
-export function debug(opts: Object, msg: string) {
-  debugBabel(message(opts, msg));
-}
-
-export function message(opts: Object, msg: string) {
-  // There are a few case where throws errors will try to annotate themselves multiple times, so
-  // to keep things simple we just bail out if re-wrapping the message.
-  if (/^\[BABEL\]/.test(msg)) return msg;
-
-  return `[BABEL] ${opts.filename || "unknown"}: ${msg}`;
-}
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index 6f345592c5..85c8d9eeaa 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -2,7 +2,7 @@ import * as babel from "../lib/index";
 import buildExternalHelpers from "../lib/tools/build-external-helpers";
 import sourceMap from "source-map";
 import assert from "assert";
-import Plugin from "../lib/transformation/plugin";
+import Plugin from "../lib/config/plugin";
 import generator from "babel-generator";
 
 function assertIgnored(result) {
diff --git a/packages/babel-core/test/config-chain.js b/packages/babel-core/test/config-chain.js
index a9cc6bd2e9..c50046ff1d 100644
--- a/packages/babel-core/test/config-chain.js
+++ b/packages/babel-core/test/config-chain.js
@@ -1,6 +1,6 @@
 import assert from "assert";
 import path from "path";
-import buildConfigChain from "../lib/transformation/file/options/build-config-chain";
+import buildConfigChain from "../lib/config/build-config-chain";
 
 function fixture() {
   const args = [__dirname, "fixtures", "config"];
@@ -40,6 +40,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           plugins: [
             "extended",
@@ -50,6 +51,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "root",
@@ -60,6 +62,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -70,6 +73,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("dir1", "src.js"),
         },
@@ -89,6 +93,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -99,6 +104,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "dir2",
@@ -109,6 +115,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("dir2"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("dir2", "src.js"),
         },
@@ -128,6 +135,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -138,6 +146,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "env-base",
@@ -148,6 +157,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("env"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("env", "src.js"),
         },
@@ -169,6 +179,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -179,6 +190,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "env-base",
@@ -189,6 +201,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("env"),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "env-foo",
@@ -199,6 +212,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("env"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("env", "src.js"),
         },
@@ -221,6 +235,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -231,6 +246,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "env-base",
@@ -241,6 +257,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("env"),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "env-bar",
@@ -251,6 +268,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("env"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("env", "src.js"),
         },
@@ -273,6 +291,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           plugins: ["pkg-plugin"],
         },
@@ -281,6 +300,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("pkg"),
       },
       {
+        type: "options",
         options: {
           ignore: ["pkg-ignore"],
         },
@@ -289,6 +309,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("pkg"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("pkg", "src.js"),
         },
@@ -308,6 +329,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -318,6 +340,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "foo",
@@ -329,6 +352,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("js-config"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("js-config", "src.js"),
         },
@@ -348,6 +372,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -358,6 +383,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "foo",
@@ -369,6 +395,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("js-config-default"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("js-config-default", "src.js"),
         },
@@ -387,6 +414,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -397,6 +425,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "extended",
@@ -407,6 +436,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "foo",
@@ -418,6 +448,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("js-config-extended"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("js-config-extended", "src.js"),
         },
@@ -438,6 +469,7 @@ describe("buildConfigChain", function () {
 
     const expected = [
       {
+        type: "options",
         options: {
           ignore: [
             "root-ignore",
@@ -448,6 +480,7 @@ describe("buildConfigChain", function () {
         dirname: fixture(),
       },
       {
+        type: "options",
         options: {
           plugins: [
             "json",
@@ -458,6 +491,7 @@ describe("buildConfigChain", function () {
         dirname: fixture("json-pkg-config-no-babel"),
       },
       {
+        type: "arguments",
         options: {
           filename: fixture("json-pkg-config-no-babel", "src.js"),
         },
diff --git a/packages/babel-core/test/get-possible-plugin-names.js b/packages/babel-core/test/get-possible-plugin-names.js
index 7ce8644769..d0c14e69f9 100644
--- a/packages/babel-core/test/get-possible-plugin-names.js
+++ b/packages/babel-core/test/get-possible-plugin-names.js
@@ -1,5 +1,5 @@
 import assert from "assert";
-import getPossiblePluginNames from "../lib/helpers/get-possible-plugin-names";
+import getPossiblePluginNames from "../lib/config/helpers/get-possible-plugin-names";
 
 describe("getPossiblePluginNames", function () {
   it("adds the babel-plugin prefix", function() {
diff --git a/packages/babel-core/test/get-possible-preset-names.js b/packages/babel-core/test/get-possible-preset-names.js
index 40052fdfbb..0630f0fb71 100644
--- a/packages/babel-core/test/get-possible-preset-names.js
+++ b/packages/babel-core/test/get-possible-preset-names.js
@@ -1,5 +1,5 @@
 import assert from "assert";
-import getPossiblePresetNames from "../lib/helpers/get-possible-preset-names";
+import getPossiblePresetNames from "../lib/config/helpers/get-possible-preset-names";
 
 describe("getPossiblePresetNames", function () {
   it("adds the babel-preset prefix", function() {
diff --git a/packages/babel-core/test/option-manager.js b/packages/babel-core/test/option-manager.js
index 126ed83c27..a2cfd86faf 100644
--- a/packages/babel-core/test/option-manager.js
+++ b/packages/babel-core/test/option-manager.js
@@ -1,5 +1,5 @@
 import assert from "assert";
-import OptionManager from "../lib/transformation/file/options/option-manager";
+import OptionManager from "../lib/config/option-manager";
 import path from "path";
 
 describe("option-manager", () => {
diff --git a/packages/babel-core/test/path.js b/packages/babel-core/test/path.js
index f84d7eef8e..dbc30827c5 100644
--- a/packages/babel-core/test/path.js
+++ b/packages/babel-core/test/path.js
@@ -1,5 +1,5 @@
 import { transform } from "../lib/index";
-import Plugin from "../lib/transformation/plugin";
+import Plugin from "../lib/config/plugin";
 import chai from "chai";
 
 describe("traversal path", function () {
diff --git a/packages/babel-preset-react/src/index.js b/packages/babel-preset-react/src/index.js
index 5b953685aa..99bc2eac3b 100644
--- a/packages/babel-preset-react/src/index.js
+++ b/packages/babel-preset-react/src/index.js
@@ -3,10 +3,6 @@ import transformReactJSX from "babel-plugin-transform-react-jsx";
 import transformSyntaxJSX from "babel-plugin-syntax-jsx";
 import transformReactDisplayName from "babel-plugin-transform-react-display-name";
 
-// These imports not yet used...
-// import transformReactJSXSource from "babel-plugin-transform-react-jsx-source";
-// import transformReactJSXSelf from "babel-plugin-transform-react-jsx-self";
-
 export default function () {
   return {
     presets: [
@@ -17,13 +13,5 @@ export default function () {
       transformSyntaxJSX,
       transformReactDisplayName,
     ],
-    env: {
-      development: {
-        plugins: [
-          // transformReactJSXSource,
-          // transformReactJSXSelf
-        ],
-      },
-    },
   };
 }
diff --git a/packages/babel-runtime/scripts/build-dist.js b/packages/babel-runtime/scripts/build-dist.js
index 3aee330207..5e73c94c67 100644
--- a/packages/babel-runtime/scripts/build-dist.js
+++ b/packages/babel-runtime/scripts/build-dist.js
@@ -25,7 +25,6 @@ paths.forEach(function (path) {
 
 var helpers    = require("babel-helpers");
 var babel      = require("../../babel-core");
-var util       = require("../../babel-core/lib/util");
 var t          = require("../../babel-types");
 
 function relative(filename) {
diff --git a/yarn.lock b/yarn.lock
index b730d5b88e..0fc054e20d 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1926,9 +1926,9 @@ flat-cache@^1.2.1:
     graceful-fs "^4.1.2"
     write "^0.2.1"
 
-flow-bin@^0.34.0:
-  version "0.34.0"
-  resolved "https://registry.yarnpkg.com/flow-bin/-/flow-bin-0.34.0.tgz#093ed36981e8fafc39d16f0b0878d0968aa80fad"
+flow-bin@^0.41.0:
+  version "0.41.0"
+  resolved "https://registry.yarnpkg.com/flow-bin/-/flow-bin-0.41.0.tgz#8badac9a19da45004997e599bd316518db489b2e"
 
 for-in@^0.1.5:
   version "0.1.6"