diff --git a/CHANGES.md b/CHANGES.md
index 0610d64..b0d94f7 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,7 @@
 ## UNRELEASED
  * Require node>=4.0.0.
+ * Reorganize internal directory structure. The main file moved to
+   `src/ng-annotate-main.js`.
 
 ## v1.6.0 2017-05-28
  * Switch from tilde ~ dependencies to ^ caret dependencies.
diff --git a/OPTIONS.md b/OPTIONS.md
index 17cb526..b42274b 100644
--- a/OPTIONS.md
+++ b/OPTIONS.md
@@ -29,13 +29,13 @@ controllers, etc.) with a new name when declared and referenced through annotati
 Use it like this: `--rename oldname1 newname1 oldname2 newname2`
 
 *experimental* Use the `--plugin` option to load a user plugin with the provided path,
-1.x may change API). See [plugin-example.js](plugin-example.js) for more info.
+1.x may change API). See [plugin-example.js](examples/plugin-example.js) for more info.
 
 *experimental* Use the `--stats` option to print statistics on stderr.
 
 
 ## Library (API)
-ng-annotate can be used as a library. See [ng-annotate.js](ng-annotate.js) for further info about
+ng-annotate can be used as a library. See [ng-annotate.js](src/ng-annotate.js) for further info about
 options and return value.
 
 ```js
diff --git a/plugin-example.js b/examples/plugin-example.js
similarity index 100%
rename from plugin-example.js
rename to examples/plugin-example.js
diff --git a/ng-annotate b/ng-annotate
index 40fb562..b78590f 100755
--- a/ng-annotate
+++ b/ng-annotate
@@ -1,2 +1,2 @@
 #!/usr/bin/env node
-require("./ng-annotate.js");
+require("./src/ng-annotate.js");
diff --git a/package.json b/package.json
index ca874b2..2c020dc 100644
--- a/package.json
+++ b/package.json
@@ -2,7 +2,7 @@
   "name": "ng-annotate-patched",
   "version": "1.6.0",
   "description": "add, remove and rebuild angularjs dependency injection annotations",
-  "main": "ng-annotate-main.js",
+  "main": "src/ng-annotate-main.js",
   "repository": {
     "type": "git",
     "url": "https://github.com/bluetech/ng-annotate-patched.git"
@@ -37,7 +37,7 @@
     "transformation"
   ],
   "scripts": {
-    "test": "node run-tests"
+    "test": "node tests/run-tests"
   },
   "bin": "./ng-annotate",
   "author": "Olov Lassus <olov.lassus@gmail.com>",
diff --git a/generate-sourcemap.js b/src/generate-sourcemap.js
similarity index 100%
rename from generate-sourcemap.js
rename to src/generate-sourcemap.js
diff --git a/lut.js b/src/lut.js
similarity index 100%
rename from lut.js
rename to src/lut.js
diff --git a/ng-annotate-main.js b/src/ng-annotate-main.js
similarity index 100%
rename from ng-annotate-main.js
rename to src/ng-annotate-main.js
diff --git a/ng-annotate.js b/src/ng-annotate.js
similarity index 99%
rename from ng-annotate.js
rename to src/ng-annotate.js
index d8af793..5b16ce7 100644
--- a/ng-annotate.js
+++ b/src/ng-annotate.js
@@ -9,7 +9,7 @@ const fs = require("fs");
 const fmt = require("simple-fmt");
 const tryor = require("tryor");
 const ngAnnotate = require("./ng-annotate-main");
-const version = require("./package.json").version;
+const version = require("../package.json").version;
 const optimist = require("optimist")
     .usage("ng-annotate v" + version + "\n\nUsage: ng-annotate OPTIONS <file>\n\n" +
         "provide - instead of <file> to read from stdin\n" +
diff --git a/nginject.js b/src/nginject.js
similarity index 100%
rename from nginject.js
rename to src/nginject.js
diff --git a/optionals/angular-dashboard-framework.js b/src/optionals/angular-dashboard-framework.js
similarity index 100%
rename from optionals/angular-dashboard-framework.js
rename to src/optionals/angular-dashboard-framework.js
diff --git a/pos-to-linecolumn.js b/src/pos-to-linecolumn.js
similarity index 100%
rename from pos-to-linecolumn.js
rename to src/pos-to-linecolumn.js
diff --git a/scope.js b/src/scope.js
similarity index 100%
rename from scope.js
rename to src/scope.js
diff --git a/scopetools.js b/src/scopetools.js
similarity index 100%
rename from scopetools.js
rename to src/scopetools.js
diff --git a/traverse.js b/src/traverse.js
similarity index 100%
rename from traverse.js
rename to src/traverse.js
diff --git a/run-tests.js b/tests/run-tests.js
similarity index 98%
rename from run-tests.js
rename to tests/run-tests.js
index edc4383..b123e70 100644
--- a/run-tests.js
+++ b/tests/run-tests.js
@@ -4,7 +4,7 @@
 
 "use strict";
 
-const ngAnnotate = require("./ng-annotate-main");
+const ngAnnotate = require("../src/ng-annotate-main");
 const fs = require("fs");
 const os = require("os");
 const path = require("path");
@@ -16,7 +16,7 @@ const coffee = require("coffee-script");
 const convertSourceMap = require("convert-source-map");
 
 // optionals
-const ngAnnotateAdfPlugin = require("./optionals/angular-dashboard-framework.js");
+const ngAnnotateAdfPlugin = require("../src/optionals/angular-dashboard-framework.js");
 
 function slurp(filename) {
     return String(fs.readFileSync(filename));