diff --git a/.flowconfig b/.flowconfig
index ba9239f778..9097683673 100644
--- a/.flowconfig
+++ b/.flowconfig
@@ -15,3 +15,4 @@ lib/third-party-libs.js.flow
 [options]
 suppress_comment= \\(.\\|\n\\)*\\$FlowFixMe
 suppress_comment= \\(.\\|\n\\)*\\$FlowIssue
+esproposal.export_star_as=enable
diff --git a/lib/third-party-libs.js.flow b/lib/third-party-libs.js.flow
index 1aefc40618..97d19dfda2 100644
--- a/lib/third-party-libs.js.flow
+++ b/lib/third-party-libs.js.flow
@@ -31,3 +31,36 @@ declare module "lodash/clone" {
 declare module "lodash/merge" {
   declare export default <T: Object>(T, Object) => T;
 }
+
+declare module "convert-source-map" {
+  declare export type SourceMap = {
+    version: 3,
+    file: ?string,
+    sources: [?string],
+    sourcesContent: [?string],
+    names: [?string],
+    mappings: string,
+  };
+
+  declare class Converter {
+    toJSON(): string;
+    toBase64(): string;
+    toComment(): string;
+    toObject(): SourceMap
+  }
+
+  declare module.exports: {
+    SourceMap: SourceMap,
+    Converter: Converter,
+    fromObject(obj: SourceMap): Converter,
+    fromJSON(str: string): Converter,
+    fromBase64(str: string): Converter,
+    fromComment(str: string): Converter,
+    fromMapFileComment(str: string): Converter,
+    fromSource(str: string): Converter,
+    fromMapFileSource(str: string): Converter,
+    removeComments(str: string): string,
+    removeMapFileComments(str: string): string,
+    generateMapFileComment(path: string, options?: ?{ multiline: boolean }): string,
+  };
+}
diff --git a/packages/babel-core/src/config/index.js b/packages/babel-core/src/config/index.js
index f00fd0e924..61684308e3 100644
--- a/packages/babel-core/src/config/index.js
+++ b/packages/babel-core/src/config/index.js
@@ -5,9 +5,13 @@ import manageOptions from "./option-manager";
 
 export type ResolvedConfig = {
   options: Object,
-  passes: Array<Array<[Plugin, ?{}]>>,
+  passes: PluginPasses,
 };
 
+export type { Plugin };
+export type PluginPassList = Array<[Plugin, ?{}]>;
+export type PluginPasses = Array<PluginPassList>;
+
 /**
  * Standard API for loading Babel configuration data. Not for public consumption.
  */
diff --git a/packages/babel-core/src/config/plugin.js b/packages/babel-core/src/config/plugin.js
index 84b3701061..58a768ffa2 100644
--- a/packages/babel-core/src/config/plugin.js
+++ b/packages/babel-core/src/config/plugin.js
@@ -1,6 +1,12 @@
 // @flow
 
 export default class Plugin {
+  key: ?string;
+  manipulateOptions: ?Function;
+  post: ?Function;
+  pre: ?Function;
+  visitor: ?{};
+
   constructor(plugin: {}, key?: string) {
     if (plugin.name != null && typeof plugin.name !== "string") {
       throw new Error("Plugin .name must be a string, null, or undefined");
@@ -30,10 +36,4 @@ export default class Plugin {
     this.pre = plugin.pre;
     this.visitor = plugin.visitor;
   }
-
-  key: ?string;
-  manipulateOptions: ?Function;
-  post: ?Function;
-  pre: ?Function;
-  visitor: ?{};
 }
diff --git a/packages/babel-core/src/index.js b/packages/babel-core/src/index.js
index 998bbd835f..4281a15976 100644
--- a/packages/babel-core/src/index.js
+++ b/packages/babel-core/src/index.js
@@ -1,17 +1,20 @@
-export File from "./transformation/file";
-export buildExternalHelpers from "./tools/build-external-helpers";
+// @flow
+
+export {
+  default as buildExternalHelpers,
+} from "./tools/build-external-helpers";
 export { resolvePlugin, resolvePreset } from "./config/loading/files";
 
 export { version } from "../package";
 export { getEnv } from "./config/helpers/environment";
 
 export * as types from "babel-types";
-export traverse from "babel-traverse";
-export template from "babel-template";
+export { default as traverse } from "babel-traverse";
+export { default as template } from "babel-template";
 
 import loadConfig from "./config";
 
-export function loadOptions(opts): Object | null {
+export function loadOptions(opts: {}): Object | null {
   const config = loadConfig(opts);
 
   return config ? config.options : null;
@@ -19,21 +22,21 @@ export function loadOptions(opts): Object | null {
 
 // For easier backward-compatibility, provide an API like the one we exposed in Babel 6.
 export class OptionManager {
-  init(opts) {
+  init(opts: {}) {
     return loadOptions(opts);
   }
 }
 
-export function Plugin(alias) {
-  throw new Error(`The (${alias}) Babel 5 plugin is being run with Babel 6.`);
+export function Plugin(alias: string) {
+  throw new Error(
+    `The (${alias}) Babel 5 plugin is being run with an unsupported Babel version.`,
+  );
 }
 
-export {
-  transform,
-  transformFromAst,
-  transformFile,
-  transformFileSync,
-} from "./transformation";
+export { default as transform } from "./transform";
+export { default as transformFromAst } from "./transform-ast";
+export { default as transformFile } from "./transform-file";
+export { default as transformFileSync } from "./transform-file-sync";
 
 /**
  * Recommended set of compilable extensions. Not used in babel-core directly, but meant as
diff --git a/packages/babel-core/src/transform-ast.js b/packages/babel-core/src/transform-ast.js
new file mode 100644
index 0000000000..85b94063b8
--- /dev/null
+++ b/packages/babel-core/src/transform-ast.js
@@ -0,0 +1,21 @@
+// @flow
+import * as t from "babel-types";
+import loadConfig from "./config";
+import runTransform, { type FileResult } from "./transformation";
+
+export default function transformFromAst(
+  ast: Object,
+  code: string,
+  opts: Object,
+): FileResult | null {
+  const config = loadConfig(opts);
+  if (config === null) return null;
+
+  if (ast && ast.type === "Program") {
+    ast = t.file(ast, [], []);
+  } else if (!ast || ast.type !== "File") {
+    throw new Error("Not a valid ast?");
+  }
+
+  return runTransform(config, code, ast);
+}
diff --git a/packages/babel-core/src/transform-file-sync.js b/packages/babel-core/src/transform-file-sync.js
new file mode 100644
index 0000000000..d0a2d2823b
--- /dev/null
+++ b/packages/babel-core/src/transform-file-sync.js
@@ -0,0 +1,16 @@
+// @flow
+import fs from "fs";
+
+import loadConfig from "./config";
+import runTransform, { type FileResult } from "./transformation";
+
+export default function transformFileSync(
+  filename: string,
+  opts?: Object = {},
+): FileResult | null {
+  opts.filename = filename;
+  const config = loadConfig(opts);
+  if (config === null) return null;
+
+  return runTransform(config, fs.readFileSync(filename, "utf8"));
+}
diff --git a/packages/babel-core/src/transform-file.js b/packages/babel-core/src/transform-file.js
new file mode 100644
index 0000000000..71f576be09
--- /dev/null
+++ b/packages/babel-core/src/transform-file.js
@@ -0,0 +1,32 @@
+// @flow
+import fs from "fs";
+
+import loadConfig from "./config";
+import runTransform, { type FileResult } from "./transformation";
+
+export default function transformFile(
+  filename: string,
+  opts?: Object = {},
+  callback: (?Error, FileResult | null) => void,
+) {
+  if (typeof opts === "function") {
+    callback = opts;
+    opts = {};
+  }
+
+  opts.filename = filename;
+  const config = loadConfig(opts);
+  if (config === null) return callback(null, null);
+
+  fs.readFile(filename, "utf8", function(err, code: string) {
+    if (err) return callback(err, null);
+
+    let result;
+    try {
+      result = runTransform(config, code);
+    } catch (_err) {
+      return callback(err, null);
+    }
+    callback(null, result);
+  });
+}
diff --git a/packages/babel-core/src/transform.js b/packages/babel-core/src/transform.js
new file mode 100644
index 0000000000..cfea9983c7
--- /dev/null
+++ b/packages/babel-core/src/transform.js
@@ -0,0 +1,13 @@
+// @flow
+import loadConfig from "./config";
+import runTransform, { type FileResult } from "./transformation";
+
+export default function transform(
+  code: string,
+  opts?: Object,
+): FileResult | null {
+  const config = loadConfig(opts);
+  if (config === null) return null;
+
+  return runTransform(config, code);
+}
diff --git a/packages/babel-core/src/transformation/internal-plugins/block-hoist.js b/packages/babel-core/src/transformation/block-hoist-plugin.js
similarity index 60%
rename from packages/babel-core/src/transformation/internal-plugins/block-hoist.js
rename to packages/babel-core/src/transformation/block-hoist-plugin.js
index 1682670314..f307c09e89 100644
--- a/packages/babel-core/src/transformation/internal-plugins/block-hoist.js
+++ b/packages/babel-core/src/transformation/block-hoist-plugin.js
@@ -1,6 +1,28 @@
+// @flow
+
 import sortBy from "lodash/sortBy";
 
-export default {
+import loadConfig, { type Plugin } from "../config";
+
+let LOADED_PLUGIN: Plugin | void;
+
+export default function loadBlockHoistPlugin(): [Plugin, void] {
+  if (!LOADED_PLUGIN) {
+    // Lazy-init the internal plugin to remove the init-time circular
+    // dependency between plugins being passed babel-core's export object,
+    // which loads this file, and this 'loadConfig' loading plugins.
+    const config = loadConfig({
+      babelrc: false,
+      plugins: [blockHoistPlugin],
+    });
+    LOADED_PLUGIN = config ? config.passes[0][0][0] : undefined;
+    if (!LOADED_PLUGIN) throw new Error("Assertion failure");
+  }
+
+  return [LOADED_PLUGIN, undefined];
+}
+
+const blockHoistPlugin = {
   /**
    * [Please add a description.]
    *
diff --git a/packages/babel-core/src/transformation/file/file.js b/packages/babel-core/src/transformation/file/file.js
new file mode 100644
index 0000000000..aec4db3c04
--- /dev/null
+++ b/packages/babel-core/src/transformation/file/file.js
@@ -0,0 +1,212 @@
+// @flow
+
+import getHelper from "babel-helpers";
+import { NodePath, Hub, Scope } from "babel-traverse";
+import { codeFrameColumns } from "babel-code-frame";
+import traverse from "babel-traverse";
+import * as t from "babel-types";
+
+import type { NormalizedFile } from "../normalize-file";
+
+const errorVisitor = {
+  enter(path, state) {
+    const loc = path.node.loc;
+    if (loc) {
+      state.loc = loc;
+      path.stop();
+    }
+  },
+};
+
+export default class File {
+  _map: Map<any, any> = new Map();
+  opts: Object;
+  declarations: Object = {};
+  path: NodePath = null;
+  ast: Object = {};
+  scope: Scope;
+  metadata: {} = {};
+  hub: Hub = new Hub(this);
+  code: string = "";
+  shebang: string | null = "";
+  inputMap: Object | null = null;
+
+  constructor(options: {}, { code, ast, shebang, inputMap }: NormalizedFile) {
+    this.opts = options;
+    this.code = code;
+    this.ast = ast;
+    this.shebang = shebang;
+    this.inputMap = inputMap;
+
+    this.path = NodePath.get({
+      hub: this.hub,
+      parentPath: null,
+      parent: this.ast,
+      container: this.ast,
+      key: "program",
+    }).setContext();
+    this.scope = this.path.scope;
+  }
+
+  set(key: mixed, val: mixed) {
+    this._map.set(key, val);
+  }
+
+  get(key: mixed): any {
+    return this._map.get(key);
+  }
+
+  getModuleName(): ?string {
+    const opts = this.opts;
+    if (!opts.moduleIds) {
+      return null;
+    }
+
+    // moduleId is n/a if a `getModuleId()` is provided
+    if (opts.moduleId != null && !opts.getModuleId) {
+      return opts.moduleId;
+    }
+
+    let filenameRelative = opts.filenameRelative;
+    let moduleName = "";
+
+    if (opts.moduleRoot != null) {
+      moduleName = opts.moduleRoot + "/";
+    }
+
+    if (!opts.filenameRelative) {
+      return moduleName + opts.filename.replace(/^\//, "");
+    }
+
+    if (opts.sourceRoot != null) {
+      // remove sourceRoot from filename
+      const sourceRootRegEx = new RegExp("^" + opts.sourceRoot + "/?");
+      filenameRelative = filenameRelative.replace(sourceRootRegEx, "");
+    }
+
+    // remove extension
+    filenameRelative = filenameRelative.replace(/\.(\w*?)$/, "");
+
+    moduleName += filenameRelative;
+
+    // normalize path separators
+    moduleName = moduleName.replace(/\\/g, "/");
+
+    if (opts.getModuleId) {
+      // If return is falsy, assume they want us to use our generated default name
+      return opts.getModuleId(moduleName) || moduleName;
+    } else {
+      return moduleName;
+    }
+  }
+
+  // TODO: Remove this before 7.x's official release. Leaving it in for now to
+  // prevent unnecessary breakage between beta versions.
+  resolveModuleSource(source: string): string {
+    return source;
+  }
+
+  addImport() {
+    throw new Error(
+      "This API has been removed. If you're looking for this " +
+        "functionality in Babel 7, you should import the " +
+        "'babel-helper-module-imports' module and use the functions exposed " +
+        " from that module, such as 'addNamed' or 'addDefault'.",
+    );
+  }
+
+  addHelper(name: string): Object {
+    const declar = this.declarations[name];
+    if (declar) return declar;
+
+    const generator = this.get("helperGenerator");
+    const runtime = this.get("helpersNamespace");
+    if (generator) {
+      const res = generator(name);
+      if (res) return res;
+    } else if (runtime) {
+      return t.memberExpression(runtime, t.identifier(name));
+    }
+
+    const uid = (this.declarations[name] = this.scope.generateUidIdentifier(
+      name,
+    ));
+
+    const { nodes, globals } = getHelper(
+      name,
+      name => this.addHelper(name),
+      uid,
+      () => Object.keys(this.scope.getAllBindings()),
+    );
+
+    globals.forEach(name => {
+      if (this.path.scope.hasBinding(name, true /* noGlobals */)) {
+        this.path.scope.rename(name);
+      }
+    });
+
+    nodes.forEach(node => {
+      node._compact = true;
+    });
+
+    this.path.unshiftContainer("body", nodes);
+    // TODO: NodePath#unshiftContainer should automatically register new
+    // bindings.
+    this.path.get("body").forEach(path => {
+      if (nodes.indexOf(path.node) === -1) return;
+      if (path.isVariableDeclaration()) this.scope.registerDeclaration(path);
+    });
+
+    return uid;
+  }
+
+  addTemplateObject() {
+    throw new Error(
+      "This function has been moved into the template literal transform itself.",
+    );
+  }
+
+  buildCodeFrameError(
+    node: ?{
+      loc?: { line: number, column: number },
+      _loc?: { line: number, column: number },
+    },
+    msg: string,
+    Error: typeof Error = SyntaxError,
+  ): Error {
+    let loc = node && (node.loc || node._loc);
+
+    msg = `${this.opts.filename}: ${msg}`;
+
+    if (!loc && node) {
+      const state = {
+        loc: null,
+      };
+      traverse(node, errorVisitor, this.scope, state);
+      loc = state.loc;
+
+      let txt =
+        "This is an error on an internal node. Probably an internal error.";
+      if (loc) txt += " Location has been estimated.";
+
+      msg += ` (${txt})`;
+    }
+
+    if (loc) {
+      msg +=
+        "\n" +
+        codeFrameColumns(
+          this.code,
+          {
+            start: {
+              line: loc.line,
+              column: loc.column + 1,
+            },
+          },
+          this.opts,
+        );
+    }
+
+    return new Error(msg);
+  }
+}
diff --git a/packages/babel-core/src/transformation/file/generate.js b/packages/babel-core/src/transformation/file/generate.js
new file mode 100644
index 0000000000..4601106561
--- /dev/null
+++ b/packages/babel-core/src/transformation/file/generate.js
@@ -0,0 +1,89 @@
+// @flow
+
+import convertSourceMap, { type SourceMap } from "convert-source-map";
+import sourceMap from "source-map";
+import generate from "babel-generator";
+
+import type File from "./file";
+
+export default function generateCode(
+  file: File,
+): {
+  outputCode: string,
+  outputMap: SourceMap | null,
+} {
+  const { opts, ast, shebang, code, inputMap } = file;
+
+  let gen = generate;
+  if (opts.generatorOpts && opts.generatorOpts.generator) {
+    gen = opts.generatorOpts.generator;
+  }
+
+  let { code: outputCode, map: outputMap } = gen(
+    ast,
+    opts.generatorOpts ? Object.assign(opts, opts.generatorOpts) : opts,
+    code,
+  );
+
+  if (shebang) {
+    // add back shebang
+    outputCode = `${shebang}\n${outputCode}`;
+  }
+
+  if (outputMap && inputMap) {
+    outputMap = mergeSourceMap(inputMap.toObject(), outputMap);
+  }
+
+  if (opts.sourceMaps === "inline" || opts.sourceMaps === "both") {
+    outputCode += "\n" + convertSourceMap.fromObject(outputMap).toComment();
+  }
+
+  if (opts.sourceMaps === "inline") {
+    outputMap = null;
+  }
+
+  return { outputCode, outputMap };
+}
+
+function mergeSourceMap(inputMap: SourceMap, map: SourceMap): SourceMap {
+  const inputMapConsumer = new sourceMap.SourceMapConsumer(inputMap);
+  const outputMapConsumer = new sourceMap.SourceMapConsumer(map);
+
+  const mergedGenerator = new sourceMap.SourceMapGenerator({
+    file: inputMapConsumer.file,
+    sourceRoot: inputMapConsumer.sourceRoot,
+  });
+
+  // This assumes the output map always has a single source, since Babel always compiles a
+  // single source file to a single output file.
+  const source = outputMapConsumer.sources[0];
+
+  inputMapConsumer.eachMapping(function(mapping) {
+    const generatedPosition = outputMapConsumer.generatedPositionFor({
+      line: mapping.generatedLine,
+      column: mapping.generatedColumn,
+      source: source,
+    });
+    if (generatedPosition.column != null) {
+      mergedGenerator.addMapping({
+        source: mapping.source,
+
+        original:
+          mapping.source == null
+            ? null
+            : {
+                line: mapping.originalLine,
+                column: mapping.originalColumn,
+              },
+
+        generated: generatedPosition,
+
+        name: mapping.name,
+      });
+    }
+  });
+
+  const mergedMap = mergedGenerator.toJSON();
+  inputMap.mappings = mergedMap.mappings;
+  return inputMap;
+}
diff --git a/packages/babel-core/src/transformation/file/index.js b/packages/babel-core/src/transformation/file/index.js
deleted file mode 100644
index c0538464f4..0000000000
--- a/packages/babel-core/src/transformation/file/index.js
+++ /dev/null
@@ -1,501 +0,0 @@
-/* global BabelFileResult, BabelParserOptions, BabelFileMetadata */
-
-import getHelper from "babel-helpers";
-import convertSourceMap from "convert-source-map";
-import PluginPass from "../plugin-pass";
-import { NodePath, Hub, Scope } from "babel-traverse";
-import sourceMap from "source-map";
-import generate from "babel-generator";
-import { codeFrameColumns } from "babel-code-frame";
-import traverse from "babel-traverse";
-import { parse } from "babylon";
-import * as t from "babel-types";
-import buildDebug from "debug";
-
-import loadConfig, { type ResolvedConfig } from "../../config";
-
-import blockHoistPlugin from "../internal-plugins/block-hoist";
-
-const babelDebug = buildDebug("babel:file");
-
-export function debug(opts: Object, msg: string) {
-  babelDebug(`${opts.filename || "unknown"}: ${msg}`);
-}
-
-const shebangRegex = /^#!.*/;
-
-let INTERNAL_PLUGINS;
-
-const errorVisitor = {
-  enter(path, state) {
-    const loc = path.node.loc;
-    if (loc) {
-      state.loc = loc;
-      path.stop();
-    }
-  },
-};
-
-export default class File {
-  constructor({ options, passes }: ResolvedConfig) {
-    if (!INTERNAL_PLUGINS) {
-      // Lazy-init the internal plugin to remove the init-time circular dependency between plugins being
-      // passed babel-core's export object, which loads this file, and this 'loadConfig' loading plugins.
-      INTERNAL_PLUGINS = loadConfig({
-        babelrc: false,
-        plugins: [blockHoistPlugin],
-      }).passes[0];
-    }
-
-    this._map = new Map();
-    this.pluginPasses = passes;
-    this.opts = options;
-
-    this.parserOpts = {
-      sourceType: this.opts.sourceType,
-      sourceFileName: this.opts.filename,
-      plugins: [],
-    };
-
-    for (const pluginPairs of passes) {
-      for (const [plugin] of pluginPairs) {
-        if (plugin.manipulateOptions) {
-          plugin.manipulateOptions(this.opts, this.parserOpts, this);
-        }
-      }
-    }
-
-    this.metadata = {};
-    this.declarations = {};
-
-    this.path = null;
-    this.ast = {};
-
-    this.code = "";
-    this.shebang = "";
-
-    this.hub = new Hub(this);
-  }
-
-  pluginPasses: Array<Array<[Plugin, Object]>>;
-  parserOpts: BabelParserOptions;
-  opts: Object;
-  declarations: Object;
-  path: NodePath;
-  ast: Object;
-  scope: Scope;
-  metadata: BabelFileMetadata;
-  hub: Hub;
-  code: string;
-  shebang: string;
-
-  set(key: string, val) {
-    this._map.set(key, val);
-  }
-
-  get(key: string): any {
-    return this._map.get(key);
-  }
-
-  getModuleName(): ?string {
-    const opts = this.opts;
-    if (!opts.moduleIds) {
-      return null;
-    }
-
-    // moduleId is n/a if a `getModuleId()` is provided
-    if (opts.moduleId != null && !opts.getModuleId) {
-      return opts.moduleId;
-    }
-
-    let filenameRelative = opts.filenameRelative;
-    let moduleName = "";
-
-    if (opts.moduleRoot != null) {
-      moduleName = opts.moduleRoot + "/";
-    }
-
-    if (!opts.filenameRelative) {
-      return moduleName + opts.filename.replace(/^\//, "");
-    }
-
-    if (opts.sourceRoot != null) {
-      // remove sourceRoot from filename
-      const sourceRootRegEx = new RegExp("^" + opts.sourceRoot + "/?");
-      filenameRelative = filenameRelative.replace(sourceRootRegEx, "");
-    }
-
-    // remove extension
-    filenameRelative = filenameRelative.replace(/\.(\w*?)$/, "");
-
-    moduleName += filenameRelative;
-
-    // normalize path separators
-    moduleName = moduleName.replace(/\\/g, "/");
-
-    if (opts.getModuleId) {
-      // If return is falsy, assume they want us to use our generated default name
-      return opts.getModuleId(moduleName) || moduleName;
-    } else {
-      return moduleName;
-    }
-  }
-
-  // TODO: Remove this before 7.x's official release. Leaving it in for now to
-  // prevent unnecessary breakage between beta versions.
-  resolveModuleSource(source: string): string {
-    return source;
-  }
-
-  addImport() {
-    throw new Error(
-      "This API has been removed. If you're looking for this " +
-        "functionality in Babel 7, you should import the " +
-        "'babel-helper-module-imports' module and use the functions exposed " +
-        " from that module, such as 'addNamed' or 'addDefault'.",
-    );
-  }
-
-  addHelper(name: string): Object {
-    const declar = this.declarations[name];
-    if (declar) return declar;
-
-    const generator = this.get("helperGenerator");
-    const runtime = this.get("helpersNamespace");
-    if (generator) {
-      const res = generator(name);
-      if (res) return res;
-    } else if (runtime) {
-      return t.memberExpression(runtime, t.identifier(name));
-    }
-
-    const uid = (this.declarations[name] = this.scope.generateUidIdentifier(
-      name,
-    ));
-
-    const { nodes, globals } = getHelper(
-      name,
-      name => this.addHelper(name),
-      uid,
-      () => Object.keys(this.scope.getAllBindings()),
-    );
-
-    globals.forEach(name => {
-      if (this.path.scope.hasBinding(name, true /* noGlobals */)) {
-        this.path.scope.rename(name);
-      }
-    });
-
-    nodes.forEach(node => {
-      node._compact = true;
-    });
-
-    this.path.unshiftContainer("body", nodes);
-    // TODO: NodePath#unshiftContainer should automatically register new
-    // bindings.
-    this.path.get("body").forEach(path => {
-      if (nodes.indexOf(path.node) === -1) return;
-      if (path.isVariableDeclaration()) this.scope.registerDeclaration(path);
-    });
-
-    return uid;
-  }
-
-  addTemplateObject() {
-    throw new Error(
-      "This function has been moved into the template literal transform itself.",
-    );
-  }
-
-  buildCodeFrameError(
-    node: Object,
-    msg: string,
-    Error: typeof Error = SyntaxError,
-  ): Error {
-    let loc = node && (node.loc || node._loc);
-
-    msg = `${this.opts.filename}: ${msg}`;
-
-    if (!loc && node) {
-      const state = {
-        loc: null,
-      };
-      traverse(node, errorVisitor, this.scope, state);
-      loc = state.loc;
-
-      let txt =
-        "This is an error on an internal node. Probably an internal error.";
-      if (loc) txt += " Location has been estimated.";
-
-      msg += ` (${txt})`;
-    }
-
-    msg +=
-      "\n" +
-      codeFrameColumns(
-        this.code,
-        {
-          start: {
-            line: loc.line,
-            column: loc.column + 1,
-          },
-        },
-        this.opts,
-      );
-
-    return new Error(msg);
-  }
-
-  mergeSourceMap(map: Object) {
-    const inputMap = this.opts.inputSourceMap;
-
-    if (inputMap) {
-      const inputMapConsumer = new sourceMap.SourceMapConsumer(inputMap);
-      const outputMapConsumer = new sourceMap.SourceMapConsumer(map);
-
-      const mergedGenerator = new sourceMap.SourceMapGenerator({
-        file: inputMapConsumer.file,
-        sourceRoot: inputMapConsumer.sourceRoot,
-      });
-
-      // This assumes the output map always has a single source, since Babel always compiles a
-      // single source file to a single output file.
-      const source = outputMapConsumer.sources[0];
-
-      inputMapConsumer.eachMapping(function(mapping) {
-        const generatedPosition = outputMapConsumer.generatedPositionFor({
-          line: mapping.generatedLine,
-          column: mapping.generatedColumn,
-          source: source,
-        });
-        if (generatedPosition.column != null) {
-          mergedGenerator.addMapping({
-            source: mapping.source,
-
-            original:
-              mapping.source == null
-                ? null
-                : {
-                    line: mapping.originalLine,
-                    column: mapping.originalColumn,
-                  },
-
-            generated: generatedPosition,
-
-            name: mapping.name,
-          });
-        }
-      });
-
-      const mergedMap = mergedGenerator.toJSON();
-      inputMap.mappings = mergedMap.mappings;
-      return inputMap;
-    } else {
-      return map;
-    }
-  }
-
-  parse(code: string) {
-    let parseCode = parse;
-    let parserOpts = this.opts.parserOpts;
-
-    if (parserOpts) {
-      parserOpts = Object.assign({}, this.parserOpts, parserOpts);
-
-      if (parserOpts.parser) {
-        parseCode = parserOpts.parser;
-
-        parserOpts.parser = {
-          parse(source) {
-            return parse(source, parserOpts);
-          },
-        };
-      }
-    }
-
-    debug(this.opts, "Parse start");
-    let ast;
-    try {
-      ast = parseCode(code, parserOpts || this.parserOpts);
-    } catch (err) {
-      const loc = err.loc;
-      if (loc) {
-        err.loc = null;
-        err.message =
-          `${this.opts.filename}: ${err.message}\n` +
-          codeFrameColumns(
-            this.code,
-            {
-              start: {
-                line: loc.line,
-                column: loc.column + 1,
-              },
-            },
-            this.opts,
-          );
-      }
-      throw err;
-    }
-    debug(this.opts, "Parse stop");
-    return ast;
-  }
-
-  _addAst(ast) {
-    this.path = NodePath.get({
-      hub: this.hub,
-      parentPath: null,
-      parent: ast,
-      container: ast,
-      key: "program",
-    }).setContext();
-    this.scope = this.path.scope;
-    this.ast = ast;
-  }
-
-  addAst(ast) {
-    debug(this.opts, "Start set AST");
-    this._addAst(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.key, pluginOpts);
-
-        passPairs.push([plugin, pass]);
-        passes.push(pass);
-        visitors.push(plugin.visitor);
-      }
-
-      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);
-
-      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();
-  }
-
-  addCode(code: string) {
-    code = (code || "") + "";
-    code = this.parseInputSourceMap(code);
-    this.code = code;
-  }
-
-  parseCode() {
-    this.parseShebang();
-    const ast = this.parse(this.code);
-    this.addAst(ast);
-  }
-
-  parseInputSourceMap(code: string): string {
-    const opts = this.opts;
-
-    if (opts.inputSourceMap !== false) {
-      const inputMap = convertSourceMap.fromSource(code);
-      if (inputMap) {
-        opts.inputSourceMap = inputMap.toObject();
-        code = convertSourceMap.removeComments(code);
-      }
-    }
-
-    return code;
-  }
-
-  parseShebang() {
-    const shebangMatch = shebangRegex.exec(this.code);
-    if (shebangMatch) {
-      this.shebang = shebangMatch[0];
-      this.code = this.code.replace(shebangRegex, "");
-    }
-  }
-
-  makeResult({ code, map, ast, ignored }: BabelFileResult): BabelFileResult {
-    const result = {
-      metadata: this.metadata,
-      options: this.opts,
-      ignored: !!ignored,
-      code: null,
-      ast: null,
-      map: map || null,
-    };
-
-    if (this.opts.code) {
-      result.code = code;
-    }
-
-    if (this.opts.ast) {
-      result.ast = ast;
-    }
-
-    return result;
-  }
-
-  generate(): BabelFileResult {
-    const opts = this.opts;
-    const ast = this.ast;
-
-    const result: BabelFileResult = { ast };
-    if (!opts.code) return this.makeResult(result);
-
-    let gen = generate;
-    if (opts.generatorOpts && opts.generatorOpts.generator) {
-      gen = opts.generatorOpts.generator;
-    }
-
-    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;
-
-    debug(this.opts, "Generation end");
-
-    if (this.shebang) {
-      // add back shebang
-      result.code = `${this.shebang}\n${result.code}`;
-    }
-
-    if (result.map) {
-      result.map = this.mergeSourceMap(result.map);
-    }
-
-    if (opts.sourceMaps === "inline" || opts.sourceMaps === "both") {
-      result.code += "\n" + convertSourceMap.fromObject(result.map).toComment();
-    }
-
-    if (opts.sourceMaps === "inline") {
-      result.map = null;
-    }
-
-    return this.makeResult(result);
-  }
-}
-
-export { File };
diff --git a/packages/babel-core/src/transformation/index.js b/packages/babel-core/src/transformation/index.js
index cea1c32c53..44c281d7ff 100644
--- a/packages/babel-core/src/transformation/index.js
+++ b/packages/babel-core/src/transformation/index.js
@@ -1,88 +1,80 @@
-/* global BabelFileResult */
-import fs from "fs";
+// @flow
+import traverse from "babel-traverse";
+import type { SourceMap } from "convert-source-map";
 
-import * as t from "babel-types";
-import File from "./file";
-import loadConfig from "../config";
+import type { ResolvedConfig, PluginPasses } from "../config";
 
-export function transform(code: string, opts?: Object): BabelFileResult {
-  const config = loadConfig(opts);
-  if (config === null) return null;
+import PluginPass from "./plugin-pass";
+import loadBlockHoistPlugin from "./block-hoist-plugin";
+import normalizeOptions from "./normalize-opts";
+import normalizeFile from "./normalize-file";
 
-  const file = new File(config);
-  file.addCode(code);
-  file.parseCode(code);
-  return file.transform();
-}
+import generateCode from "./file/generate";
+import File from "./file/file";
 
-export function transformFromAst(
-  ast: Object,
+export type FileResult = {
+  metadata: {},
+  options: {},
+  ast: {} | null,
+  code: string | null,
+  map: SourceMap | null,
+};
+
+export default function runTransform(
+  config: ResolvedConfig,
   code: string,
-  opts: Object,
-): BabelFileResult {
-  const config = loadConfig(opts);
-  if (config === null) return null;
+  ast?: {},
+): FileResult {
+  const options = normalizeOptions(config);
+  const input = normalizeFile(options, code, ast);
 
-  if (ast && ast.type === "Program") {
-    ast = t.file(ast, [], []);
-  } else if (!ast || ast.type !== "File") {
-    throw new Error("Not a valid ast?");
-  }
+  const file = new File(options, input);
 
-  const file = new File(config);
-  file.addCode(code);
-  file.addAst(ast);
-  return file.transform();
+  transformFile(file, config.passes);
+
+  const { outputCode, outputMap } = options.code ? generateCode(file) : {};
+
+  return {
+    metadata: file.metadata,
+    options: options,
+    ast: options.ast ? file.ast : null,
+    code: outputCode === undefined ? null : outputCode,
+    map: outputMap === undefined ? null : outputMap,
+  };
 }
 
-export function transformFile(
-  filename: string,
-  opts?: Object,
-  callback: Function,
-) {
-  if (typeof opts === "function") {
-    callback = opts;
-    opts = {};
-  }
+function transformFile(file: File, pluginPasses: PluginPasses): void {
+  for (const pluginPairs of pluginPasses) {
+    const passPairs = [];
+    const passes = [];
+    const visitors = [];
 
-  opts.filename = filename;
-  const config = loadConfig(opts);
-  if (config === null) return callback(null, null);
+    for (const [plugin, pluginOpts] of pluginPairs.concat([
+      loadBlockHoistPlugin(),
+    ])) {
+      const pass = new PluginPass(file, plugin.key, pluginOpts);
 
-  fs.readFile(filename, function(err, code) {
-    let result;
-
-    if (!err) {
-      try {
-        const file = new File(config);
-        file.addCode(code);
-        file.parseCode(code);
-        result = file.transform();
-      } catch (_err) {
-        err = _err;
-      }
+      passPairs.push([plugin, pass]);
+      passes.push(pass);
+      visitors.push(plugin.visitor);
     }
 
-    if (err) {
-      callback(err);
-    } else {
-      callback(null, result);
+    for (const [plugin, pass] of passPairs) {
+      const fn = plugin.pre;
+      if (fn) fn.call(pass, file);
     }
-  });
-}
-
-export function transformFileSync(
-  filename: string,
-  opts?: Object = {},
-): string {
-  opts.filename = filename;
-  const config = loadConfig(opts);
-  if (config === null) return null;
-
-  const code = fs.readFileSync(filename, "utf8");
-  const file = new File(config);
-
-  file.addCode(code);
-  file.parseCode(code);
-  return file.transform();
+
+    // merge all plugin visitors into a single visitor
+    const visitor = traverse.visitors.merge(
+      visitors,
+      passes,
+      file.opts.wrapPluginVisitorMethod,
+    );
+    traverse(file.ast, visitor, file.scope);
+
+    for (const [plugin, pass] of passPairs) {
+      const fn = plugin.post;
+      if (fn) fn.call(pass, file);
+    }
+  }
 }
diff --git a/packages/babel-core/src/transformation/normalize-file.js b/packages/babel-core/src/transformation/normalize-file.js
new file mode 100644
index 0000000000..7c60c2aa27
--- /dev/null
+++ b/packages/babel-core/src/transformation/normalize-file.js
@@ -0,0 +1,87 @@
+// @flow
+
+import convertSourceMap, { typeof Converter } from "convert-source-map";
+import { parse } from "babylon";
+import { codeFrameColumns } from "babel-code-frame";
+
+const shebangRegex = /^#!.*/;
+
+export type NormalizedFile = {
+  code: string,
+  ast: {},
+  shebang: string | null,
+  inputMap: Converter | null,
+};
+
+export default function normalizeFile(
+  options: Object,
+  code: string,
+  ast?: {},
+): NormalizedFile {
+  code = `${code || ""}`;
+
+  let shebang = null;
+  let inputMap = null;
+  if (options.inputSourceMap !== false) {
+    inputMap = convertSourceMap.fromSource(code);
+    if (inputMap) {
+      code = convertSourceMap.removeComments(code);
+    } else if (typeof options.inputSourceMap === "object") {
+      inputMap = convertSourceMap.fromObject(options.inputSourceMap);
+    }
+  }
+
+  const shebangMatch = shebangRegex.exec(code);
+  if (shebangMatch) {
+    shebang = shebangMatch[0];
+    code = code.replace(shebangRegex, "");
+  }
+
+  if (!ast) ast = parser(options, code);
+
+  return {
+    code,
+    ast,
+    shebang,
+    inputMap,
+  };
+}
+
+function parser(options, code) {
+  let parseCode = parse;
+
+  let { parserOpts } = options;
+  if (parserOpts.parser) {
+    parseCode = parserOpts.parser;
+
+    parserOpts = Object.assign({}, parserOpts, {
+      parser: {
+        parse(source) {
+          return parse(source, parserOpts);
+        },
+      },
+    });
+  }
+
+  try {
+    return parseCode(code, parserOpts);
+  } catch (err) {
+    const loc = err.loc;
+    if (loc) {
+      err.loc = null;
+      err.message =
+        `${options.filename}: ${err.message}\n` +
+        codeFrameColumns(
+          code,
+          {
+            start: {
+              line: loc.line,
+              column: loc.column + 1,
+            },
+          },
+          options,
+        );
+    }
+    throw err;
+  }
+}
diff --git a/packages/babel-core/src/transformation/normalize-opts.js b/packages/babel-core/src/transformation/normalize-opts.js
new file mode 100644
index 0000000000..1746ce4d27
--- /dev/null
+++ b/packages/babel-core/src/transformation/normalize-opts.js
@@ -0,0 +1,26 @@
+// @flow
+
+import type { ResolvedConfig } from "../config";
+
+export default function normalizeOptions(config: ResolvedConfig): {} {
+  const options = Object.assign({}, config.options, {
+    parserOpts: Object.assign(
+      {
+        sourceType: config.options.sourceType,
+        sourceFileName: config.options.filename,
+        plugins: [],
+      },
+      config.options.parserOpts,
+    ),
+  });
+
+  for (const pluginPairs of config.passes) {
+    for (const [plugin] of pluginPairs) {
+      if (plugin.manipulateOptions) {
+        plugin.manipulateOptions(options, options.parserOpts);
+      }
+    }
+  }
+
+  return options;
+}
diff --git a/packages/babel-core/src/transformation/plugin-pass.js b/packages/babel-core/src/transformation/plugin-pass.js
index edde9acd07..000f7e4c62 100644
--- a/packages/babel-core/src/transformation/plugin-pass.js
+++ b/packages/babel-core/src/transformation/plugin-pass.js
@@ -1,39 +1,47 @@
-import File from "./file";
+// @flow
+
+import type File from "./file/file";
 
 export default class PluginPass {
-  constructor(file: File, key: string, options: Object = {}) {
-    this._map = new Map();
-
-    this.key = key;
-    this.file = file;
-    this.opts = options;
-  }
-
-  key: string;
+  _map: Map<mixed, mixed> = new Map();
+  key: ?string;
   file: File;
   opts: Object;
 
-  set(key: string, val) {
+  constructor(file: File, key: ?string, options: ?Object) {
+    this.key = key;
+    this.file = file;
+    this.opts = options || {};
+  }
+
+  set(key: mixed, val: mixed) {
     this._map.set(key, val);
   }
 
-  get(key: string): any {
+  get(key: mixed): any {
     return this._map.get(key);
   }
 
-  addHelper(...args) {
-    return this.file.addHelper(...args);
+  addHelper(name: string) {
+    return this.file.addHelper(name);
   }
 
-  addImport(...args) {
-    return this.file.addImport(...args);
+  addImport() {
+    return this.file.addImport();
   }
 
-  getModuleName(...args) {
-    return this.file.getModuleName(...args);
+  getModuleName(): ?string {
+    return this.file.getModuleName();
   }
 
-  buildCodeFrameError(...args) {
-    return this.file.buildCodeFrameError(...args);
+  buildCodeFrameError(
+    node: ?{
+      loc?: { line: number, column: number },
+      _loc?: { line: number, column: number },
+    },
+    msg: string,
+    Error?: typeof Error,
+  ) {
+    return this.file.buildCodeFrameError(node, msg, Error);
   }
 }
diff --git a/packages/babel-core/test/option-manager.js b/packages/babel-core/test/option-manager.js
index 5358b2f2f2..7e233a2a67 100644
--- a/packages/babel-core/test/option-manager.js
+++ b/packages/babel-core/test/option-manager.js
@@ -8,7 +8,7 @@ describe("option-manager", () => {
       manageOptions({
         plugins: [({ Plugin }) => new Plugin("object-assign", {})],
       });
-    }, /Babel 5 plugin is being run with Babel 6/);
+    }, /Babel 5 plugin is being run with an unsupported Babel/);
   });
 
   describe("mergeOptions", () => {
diff --git a/packages/babel-traverse/src/hub.js b/packages/babel-traverse/src/hub.js
index f05eaa8136..69f9406fc9 100644
--- a/packages/babel-traverse/src/hub.js
+++ b/packages/babel-traverse/src/hub.js
@@ -1,6 +1,5 @@
 export default class Hub {
-  constructor(file, options) {
+  constructor(file) {
     this.file = file;
-    this.options = options;
   }
 }