diff --git a/packages/babel-cli/test/index.js b/packages/babel-cli/test/index.js
index 2bd463282e..50dd88d0cd 100644
--- a/packages/babel-cli/test/index.js
+++ b/packages/babel-cli/test/index.js
@@ -1,4 +1,3 @@
-const includes = require("lodash/includes");
 const readdir = require("fs-readdir-recursive");
 const helper = require("@babel/helper-fixtures");
 const rimraf = require("rimraf");
@@ -51,7 +50,7 @@ const assertTest = function(stdout, stderr, opts) {
 
   if (opts.stderr) {
     if (opts.stderrContains) {
-      expect(includes(stderr, expectStderr)).toBe(true);
+      expect(stderr).toContain(expectStderr);
     } else {
       expect(stderr).toBe(expectStderr);
     }
@@ -65,7 +64,7 @@ const assertTest = function(stdout, stderr, opts) {
 
   if (opts.stdout) {
     if (opts.stdoutContains) {
-      expect(includes(stdout, expectStdout)).toBe(true);
+      expect(stdout).toContain(expectStdout);
     } else {
       expect(stdout).toBe(expectStdout);
     }
diff --git a/packages/babel-core/src/config/config-chain.js b/packages/babel-core/src/config/config-chain.js
index e185f60df7..73345d0cfb 100644
--- a/packages/babel-core/src/config/config-chain.js
+++ b/packages/babel-core/src/config/config-chain.js
@@ -46,8 +46,9 @@ export type PresetInstance = {
 };
 
 export type ConfigContext = {
-  filename: string | null,
+  filename: string | void,
   cwd: string,
+  root: string,
   envName: string,
 };
 
@@ -130,18 +131,15 @@ export function buildRootChain(
   );
   if (!programmaticChain) return null;
 
-  const { root: rootDir = ".", configFile: configFileName = true } = opts;
-  let { babelrc, babelrcRoots } = opts;
-
-  const absoluteRoot = path.resolve(context.cwd, rootDir);
-
   let configFile;
-  if (typeof configFileName === "string") {
-    configFile = loadConfig(configFileName, context.cwd, context.envName);
-  } else if (configFileName === true) {
-    configFile = findRootConfig(absoluteRoot, context.envName);
+  if (typeof opts.configFile === "string") {
+    configFile = loadConfig(opts.configFile, context.cwd, context.envName);
+  } else if (opts.configFile !== false) {
+    configFile = findRootConfig(context.root, context.envName);
   }
 
+  let { babelrc, babelrcRoots } = opts;
+
   const configFileChain = emptyChain();
   if (configFile) {
     const validatedFile = validateConfigFile(configFile);
@@ -171,7 +169,7 @@ export function buildRootChain(
   if (
     (babelrc === true || babelrc === undefined) &&
     pkgData &&
-    babelrcLoadEnabled(context, pkgData, babelrcRoots, absoluteRoot)
+    babelrcLoadEnabled(context, pkgData, babelrcRoots)
   ) {
     ({ ignore: ignoreFile, config: babelrcFile } = findRelativeConfig(
       pkgData,
@@ -214,10 +212,11 @@ function babelrcLoadEnabled(
   context: ConfigContext,
   pkgData: FilePackageData,
   babelrcRoots: BabelrcSearch | void,
-  absoluteRoot: string,
 ): boolean {
   if (typeof babelrcRoots === "boolean") return babelrcRoots;
 
+  const absoluteRoot = context.root;
+
   // Fast path to avoid having to load micromatch if the babelrc is just
   // loading in the standard root directory.
   if (babelrcRoots === undefined) {
@@ -576,7 +575,7 @@ function configFieldIsApplicable(
   test: ConfigApplicableTest,
   dirname: string,
 ): boolean {
-  if (context.filename === null) {
+  if (typeof context.filename !== "string") {
     throw new Error(
       `Configuration contains explicit test/include/exclude checks, but no filename was passed to Babel`,
     );
@@ -602,7 +601,7 @@ function shouldIgnore(
   dirname: string,
 ): boolean {
   if (ignore) {
-    if (context.filename === null) {
+    if (typeof context.filename !== "string") {
       throw new Error(
         `Configuration contains ignore checks, but no filename was passed to Babel`,
       );
@@ -621,7 +620,7 @@ function shouldIgnore(
   }
 
   if (only) {
-    if (context.filename === null) {
+    if (typeof context.filename !== "string") {
       throw new Error(
         `Configuration contains ignore checks, but no filename was passed to Babel`,
       );
@@ -696,7 +695,7 @@ function matchesPatterns(
 
 const getPossibleDirs = makeWeakCache((context: ConfigContextNamed) => {
   let current = context.filename;
-  if (current === null) return [];
+  if (typeof current !== "string") return [];
 
   const possibleDirs = [current];
   while (true) {
diff --git a/packages/babel-core/src/config/partial.js b/packages/babel-core/src/config/partial.js
index c38ea87c08..0aae841ffd 100644
--- a/packages/babel-core/src/config/partial.js
+++ b/packages/babel-core/src/config/partial.js
@@ -28,12 +28,17 @@ export default function loadPrivatePartialConfig(
 
   const args = inputOpts ? validate("arguments", inputOpts) : {};
 
-  const { envName = getEnv(), cwd = "." } = args;
+  const { envName = getEnv(), cwd = ".", root: rootDir = "." } = args;
   const absoluteCwd = path.resolve(cwd);
+  const absoluteRootDir = path.resolve(absoluteCwd, rootDir);
 
   const context: ConfigContext = {
-    filename: args.filename ? path.resolve(cwd, args.filename) : null,
+    filename:
+      typeof args.filename === "string"
+        ? path.resolve(cwd, args.filename)
+        : undefined,
     cwd: absoluteCwd,
+    root: absoluteRootDir,
     envName,
   };
 
@@ -50,9 +55,14 @@ export default function loadPrivatePartialConfig(
   // to not change behavior.
   options.babelrc = false;
   options.configFile = false;
-  options.envName = envName;
-  options.cwd = absoluteCwd;
   options.passPerPreset = false;
+  options.envName = context.envName;
+  options.cwd = context.cwd;
+  options.root = context.root;
+  options.filename =
+    typeof context.filename === "string"
+      ? path.relative(context.cwd, context.filename)
+      : undefined;
 
   options.plugins = configChain.plugins.map(descriptor =>
     createItemFromDescriptor(descriptor),
diff --git a/packages/babel-core/src/transformation/plugin-pass.js b/packages/babel-core/src/transformation/plugin-pass.js
index bd44495cfe..a30803bde0 100644
--- a/packages/babel-core/src/transformation/plugin-pass.js
+++ b/packages/babel-core/src/transformation/plugin-pass.js
@@ -7,14 +7,19 @@ export default class PluginPass {
   key: ?string;
   file: File;
   opts: Object;
+
+  // The working directory that Babel's options are loaded relative to.
+  cwd: string;
+
+  // The path of the file being compiled, relative to the working directory.
   filename: string | void;
 
   constructor(file: File, key: ?string, options: ?Object) {
     this.key = key;
     this.file = file;
     this.opts = options || {};
-    this.filename =
-      typeof file.opts.filename === "string" ? file.opts.filename : undefined;
+    this.cwd = file.opts.cwd;
+    this.filename = file.opts.filename;
   }
 
   set(key: mixed, val: mixed) {
diff --git a/packages/babel-core/test/config-chain.js b/packages/babel-core/test/config-chain.js
index 63f22da52b..2d4fcedfd2 100644
--- a/packages/babel-core/test/config-chain.js
+++ b/packages/babel-core/test/config-chain.js
@@ -906,6 +906,7 @@ describe("buildConfigChain", function() {
       babelrc: false,
       configFile: false,
       cwd: process.cwd(),
+      root: process.cwd(),
       envName: "development",
       passPerPreset: false,
       plugins: [],
@@ -935,8 +936,9 @@ describe("buildConfigChain", function() {
         }),
       ).toEqual({
         ...getDefaults(),
-        filename,
+        filename: path.basename(filename),
         cwd: path.dirname(filename),
+        root: path.dirname(filename),
         comments: true,
       });
     });
@@ -946,8 +948,9 @@ describe("buildConfigChain", function() {
 
       expect(loadOptions({ filename, cwd: path.dirname(filename) })).toEqual({
         ...getDefaults(),
-        filename,
+        filename: path.basename(filename),
         cwd: path.dirname(filename),
+        root: path.dirname(filename),
         comments: true,
       });
     });
@@ -957,8 +960,9 @@ describe("buildConfigChain", function() {
 
       expect(loadOptions({ filename, cwd: path.dirname(filename) })).toEqual({
         ...getDefaults(),
-        filename,
+        filename: path.basename(filename),
         cwd: path.dirname(filename),
+        root: path.dirname(filename),
         comments: true,
       });
     });
@@ -998,8 +1002,9 @@ describe("buildConfigChain", function() {
 
       expect(loadOptions({ filename, cwd: path.dirname(filename) })).toEqual({
         ...getDefaults(),
-        filename,
+        filename: path.basename(filename),
         cwd: path.dirname(filename),
+        root: path.dirname(filename),
         comments: true,
       });
     });
diff --git a/packages/babel-plugin-transform-react-jsx-source/test/fixtures/react-source/basic-sample/exec.js b/packages/babel-plugin-transform-react-jsx-source/test/fixtures/react-source/basic-sample/exec.js
index e44c3e5e7e..397fa2915c 100644
--- a/packages/babel-plugin-transform-react-jsx-source/test/fixtures/react-source/basic-sample/exec.js
+++ b/packages/babel-plugin-transform-react-jsx-source/test/fixtures/react-source/basic-sample/exec.js
@@ -1,10 +1,10 @@
 var actual = transform(
   'var x = <sometag />',
-  Object.assign({}, opts, { filename: '/fake/path/mock.js' })
+  Object.assign({}, opts, { filename: 'fake/path/mock.js' })
 ).code;
 
 var expected = multiline([
-  'var _jsxFileName = "/fake/path/mock.js";',
+  'var _jsxFileName = "fake/path/mock.js";',
   'var x = <sometag __source={{',
   '  fileName: _jsxFileName,',
   '  lineNumber: 1',
diff --git a/packages/babel-preset-react/test/fixtures/preset-options/development/exec.js b/packages/babel-preset-react/test/fixtures/preset-options/development/exec.js
index 5ceb5a4a01..68a2881b4b 100644
--- a/packages/babel-preset-react/test/fixtures/preset-options/development/exec.js
+++ b/packages/babel-preset-react/test/fixtures/preset-options/development/exec.js
@@ -1,10 +1,10 @@
 const actual = transform(
   '<Foo bar="baz" />',
-  Object.assign({}, opts, { filename: '/fake/path/mock.js' })
+  Object.assign({}, opts, { filename: 'fake/path/mock.js' })
 ).code;
 
 const expected = multiline([
-  'var _jsxFileName = "/fake/path/mock.js";',
+  'var _jsxFileName = "fake/path/mock.js";',
   'React.createElement(Foo, {',
   '  bar: "baz",',
   '  __source: {',