diff --git a/package.json b/package.json
index 4354df3a..ae261d97 100644
--- a/package.json
+++ b/package.json
@@ -62,6 +62,7 @@
     "chalk": "^1.1.3",
     "cross-spawn": "^5.1.0",
     "fs-extra": "^4.0.1",
+    "klaw-sync": "^4.0.0",
     "minimist": "^1.2.0",
     "rimraf": "^2.6.2",
     "slash": "^1.0.0",
diff --git a/src/makePatch.ts b/src/makePatch.ts
index 7763c3f1..cce0deee 100644
--- a/src/makePatch.ts
+++ b/src/makePatch.ts
@@ -12,6 +12,7 @@ import { getPatchFiles } from "./patchFs"
 import * as fsExtra from "fs-extra"
 import { PackageManager } from "./detectPackageManager"
 import * as slash from "slash"
+import * as klawSync from "klaw-sync"
 
 function deleteScripts(json: any) {
   delete json.scripts
@@ -120,42 +121,46 @@ export default function makePatch(
       "!/node_modules\n\n",
     )
     tmpExec("git", ["init"])
-    // don't commit package.json though
-    tmpExec("git", ["add", "-f", slash(path.join("node_modules", packageName))])
 
-    tmpExec("git", ["commit", "-m", "init"])
+    klawSync(tmpRepoPackagePath, { nodir: true })
+      .map(item => item.path.slice(`${tmpRepoPackagePath}/`.length))
+      .filter(
+        relativePath =>
+          !relativePath.match(includePaths) || relativePath.match(excludePaths),
+      )
+      .forEach(relativePath =>
+        fsExtra.removeSync(slash(path.join(tmpRepoPackagePath, relativePath))),
+      )
+
+    tmpExec("git", ["add", "-f", slash(path.join("node_modules", packageName))])
+    tmpExec("git", ["commit", "--allow-empty", "-m", "init"])
 
     // replace package with user's version
     rimraf.sync(tmpRepoPackagePath)
-    fsExtra.copySync(packagePath, tmpRepoPackagePath, { recursive: true })
+
+    klawSync(packagePath, { nodir: true })
+      .map(item => item.path.slice(`${packagePath}/`.length))
+      .filter(
+        relativePath =>
+          relativePath.match(includePaths) && !relativePath.match(excludePaths),
+      )
+      .forEach(relativePath =>
+        fsExtra.copySync(
+          slash(path.join(packagePath, relativePath)),
+          slash(path.join(tmpRepoPackagePath, relativePath)),
+        ),
+      )
 
     // stage all files
     tmpExec("git", ["add", "-f", slash(path.join("node_modules", packageName))])
 
-    // unstage any ignored files so they don't show up in the diff
-    tmpExec("git", ["diff", "--cached", "--name-only"])
-      .stdout.toString()
-      .split(/\r?\n/)
-      .filter(Boolean)
-      .forEach(fileName => {
-        const scopedFileName = fileName.slice(
-          `node_modules/${packageName}/`.length,
-        )
-        if (
-          !scopedFileName.match(includePaths) ||
-          scopedFileName.match(excludePaths)
-        ) {
-          tmpExec("git", ["reset", "HEAD", fileName])
-        }
-      })
-
     // get diff of changes
     const patch = tmpExec("git", [
       "diff",
       "--cached",
       "--no-color",
       "--ignore-space-at-eol",
-      "--no-ext-diff"
+      "--no-ext-diff",
     ]).stdout.toString()
 
     if (patch.trim() === "") {
diff --git a/typings/klaw-sync.d.ts b/typings/klaw-sync.d.ts
new file mode 100644
index 00000000..281904be
--- /dev/null
+++ b/typings/klaw-sync.d.ts
@@ -0,0 +1,17 @@
+interface Options {
+  nodir?: boolean
+  nofile?: boolean
+  depthLimit?: number
+  fs?: object
+  filter?: (item: Item) => boolean
+}
+
+interface Item {
+  path: string
+  stats: object
+}
+
+declare module "klaw-sync" {
+  const klawSync: (dir: string, opts?: Options, ls?: Item[]) => Item[]
+  export = klawSync
+}
diff --git a/yarn.lock b/yarn.lock
index a197e4c4..7babcc24 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1949,6 +1949,12 @@ kind-of@^3.0.2:
   dependencies:
     is-buffer "^1.1.5"
 
+klaw-sync@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/klaw-sync/-/klaw-sync-4.0.0.tgz#7785692ea1a320ac3dda7a6c0c22b33a30aa3b3f"
+  dependencies:
+    graceful-fs "^4.1.11"
+
 latest-version@^3.0.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/latest-version/-/latest-version-3.1.0.tgz#a205383fea322b33b5ae3b18abee0dc2f356ee15"