diff --git a/CHANGELOG-4.md b/CHANGELOG-4.md
index 91f8025dc..3e1310941 100644
--- a/CHANGELOG-4.md
+++ b/CHANGELOG-4.md
@@ -7,6 +7,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+## [4.0.10] - 2023-02-05
+
+### Added
+
+- `options.cli` flag to prevent `node-glob` from globbing already globbed files and erroring out with a `package.json not found in srcDir file glob patterns` message.
+
+### Changed
+
+- Copy subdirectories of `options.srDir` in the correct location.
+
 ## [4.0.9] - 2023-02-03
 
 ### Added
diff --git a/README.md b/README.md
index 15051c4da..8ec754293 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,7 @@ nwbuild({
 CLI usage
 
 ```shell
-nwbuild ./nwapp --mode=run --version=latest --flavor=sdk
+nwbuild ./nwapp/**/* --mode=run --version=latest --flavor=sdk
 ```
 
 package.json usage
@@ -83,7 +83,7 @@ nwbuild({
 CLI usage
 
 ```shell
-nwbuild ./nwapp --mode=build --version=latest --flavor=normal --platform=linux --arch=x64 --outDir=./out
+nwbuild ./nwapp/**/* --mode=build --version=latest --flavor=normal --platform=linux --arch=x64 --outDir=./out
 ```
 
 package.json usage
@@ -301,7 +301,7 @@ The final code should look like this.
 const { nwbuild } = require("nw-builder");
 
 await nwbuild({
-  srcDir: "./nwapp",
+  srcDir: "./nwapp/**/*",
   mode: "build",
   version: "latest",
   flavor: "normal",
diff --git a/docs/global.html b/docs/global.html
index edf0c8d29..4cd331a4b 100644
--- a/docs/global.html
+++ b/docs/global.html
@@ -592,7 +592,7 @@ <h5 class="subsection-title">Properties:</h5>
               ><ul class="dummy"
                 ><li>
                   <a href="nwbuild.js.html">nwbuild.js</a>,
-                  <a href="nwbuild.js.html#line18">line 18</a>
+                  <a href="nwbuild.js.html#line17">line 17</a>
                 </li></ul
               ></dd
             >
@@ -641,7 +641,8 @@ <h5 class="subsection-title">Properties:</h5>
                 <td class="default"> "./" </td>
 
                 <td class="description last"
-                  >String of glob patterns which correspond to NW app code</td
+                  >String of space separated glob patterns which correspond to
+                  NW app code</td
                 >
               </tr>
 
@@ -849,6 +850,23 @@ <h5 class="subsection-title">Properties:</h5>
                   >If true the outDir directory is zipped</td
                 >
               </tr>
+
+              <tr>
+                <td class="name"><code>cli</code></td>
+
+                <td class="type">
+                  <span class="param-type">boolean</span>
+                </td>
+
+                <td class="attributes"> &lt;optional><br /> </td>
+
+                <td class="default"> false </td>
+
+                <td class="description last"
+                  >If true the CLI is used to glob srcDir and parse other
+                  options</td
+                >
+              </tr>
             </tbody>
           </table>
 
@@ -858,7 +876,7 @@ <h5 class="subsection-title">Properties:</h5>
               ><ul class="dummy"
                 ><li>
                   <a href="nwbuild.js.html">nwbuild.js</a>,
-                  <a href="nwbuild.js.html#line58">line 58</a>
+                  <a href="nwbuild.js.html#line57">line 57</a>
                 </li></ul
               ></dd
             >
@@ -879,8 +897,8 @@ <h2><a href="index.html">Home</a></h2
 
     <footer>
       Documentation generated by
-      <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.0</a> on Fri Jan 06
-      2023 17:15:41 GMT-0500 (Eastern Standard Time)
+      <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.0</a> on Sun Feb 05
+      2023 17:00:04 GMT-0500 (Eastern Standard Time)
     </footer>
 
     <script>
diff --git a/docs/index.html b/docs/index.html
index 8396606c0..42d1950c0 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -40,8 +40,8 @@ <h2><a href="index.html">Home</a></h2
 
     <footer>
       Documentation generated by
-      <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.0</a> on Fri Jan 06
-      2023 17:15:41 GMT-0500 (Eastern Standard Time)
+      <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.0</a> on Sun Feb 05
+      2023 17:00:04 GMT-0500 (Eastern Standard Time)
     </footer>
 
     <script>
diff --git a/docs/nwbuild.js.html b/docs/nwbuild.js.html
index 3f6de1ff8..74b5b09da 100644
--- a/docs/nwbuild.js.html
+++ b/docs/nwbuild.js.html
@@ -29,10 +29,7 @@ <h1 class="page-title">Source: nwbuild.js</h1>
         <article>
           <pre
             class="prettyprint source linenums"
-          ><code>import { mkdir, readFile, rm } from "node:fs/promises";
-import { basename } from "node:path";
-
-import glob from "glob-promise";
+          ><code>import { mkdir, rm } from "node:fs/promises";
 
 import { decompress } from "./get/decompress.js";
 import { download } from "./get/download.js";
@@ -41,6 +38,8 @@ <h1 class="page-title">Source: nwbuild.js</h1>
 import { packager } from "./bld/package.js";
 import { develop } from "./run/develop.js";
 import { isCached } from "./util/cache.js";
+import { notify } from "./util/notify.js";
+import { getOptions } from "./util/options.js";
 import { parse } from "./util/parse.js";
 import { validate } from "./util/validate.js";
 
@@ -88,7 +87,7 @@ <h1 class="page-title">Source: nwbuild.js</h1>
 
 /**
  * @typedef {object} Options
- * @property {string}                       [srcDir="./"]                             String of glob patterns which correspond to NW app code
+ * @property {string}                       [srcDir="./"]                             String of space separated glob patterns which correspond to NW app code
  * @property {"run" | "build"}              [mode="build"]                            Run or build application
  * @property {"latest" | "stable" | string} [version="latest"]                        NW runtime version
  * @property {"normal" | "sdk"}             [flavor="normal"]                         NW runtime build flavor
@@ -101,6 +100,7 @@ <h1 class="page-title">Source: nwbuild.js</h1>
  * @property {App}                          app                                       Multi platform configuration options
  * @property {boolean}                      [cache=true]                              If true the existing cache is used. Otherwise it removes and redownloads it.
  * @property {boolean}                      [zip=false]                               If true the outDir directory is zipped
+ * @property {boolean}                      [cli=false]                               If true the CLI is used to glob srcDir and parse other options
  */
 
 /**
@@ -111,67 +111,24 @@ <h1 class="page-title">Source: nwbuild.js</h1>
  */
 const nwbuild = async (options) => {
   let nwDir = "";
-  let nwPkg = undefined;
   let cached;
+  let nwCached;
   let built;
   let releaseInfo = {};
-  try {
-    let files = [];
-    let patterns = options.srcDir.split(" ");
 
-    for (const pattern of patterns) {
-      let contents = await glob(pattern);
-      files.push(...contents);
-      // Try to find the first instance of the package.json
-      for (const content of contents) {
-        if (basename(content) === "package.json" &amp;&amp; nwPkg === undefined) {
-          nwPkg = JSON.parse(await readFile(content));
-        }
-      }
-
-      if (nwPkg === undefined) {
-        throw new Error("package.json not found in srcDir file glob patterns.");
-      }
-    }
+  notify();
 
-    if (files.length === 0) {
-      throw new Error(`The globbing pattern ${options.srcDir} is invalid.`);
-    }
-
-    // The name property is required for NW.js applications
-    if (nwPkg.name === undefined) {
-      throw new Error(`name property is missing from package.json`);
-    }
-
-    // The main property is required for NW.js applications
-    if (nwPkg.main === undefined) {
-      throw new Error(`main property is missing from package.json`);
-    }
-
-    // If the nwbuild property exists in srcDir/package.json, then they take precedence
-    if (typeof nwPkg.nwbuild === "object") {
-      options = { ...nwPkg.nwbuild };
-    }
-    if (typeof nwPkg.nwbuild === "undefined") {
-      log.debug(`nwbuild property is not defined in package.json`);
-    } else {
-      throw new Error(
-        `nwbuild property in the package.json is of type ${typeof nwPkg.nwbuild}. Expected type object.`,
-      );
-    }
+  try {
+    const { opts, files, nwPkg } = await getOptions(options);
+    options = opts;
 
-    // Parse options, set required values to undefined and flags with default values unless specified by user
+    // Parse options
     options = await parse(options, nwPkg);
 
-    // Variable to store nwDir file path
-    nwDir = `${options.cacheDir}/nwjs${
-      options.flavor === "sdk" ? "-sdk" : ""
-    }-v${options.version}-${options.platform}-${options.arch}`;
-
     // Create cacheDir if it does not exist
-    cached = await isCached(nwDir);
+    cached = await isCached(options.cacheDir);
     if (cached === false) {
-      await mkdir(nwDir, { recursive: true });
+      await mkdir(options.cacheDir, { recursive: true });
     }
 
     // Create outDir if it does not exist
@@ -180,23 +137,30 @@ <h1 class="page-title">Source: nwbuild.js</h1>
       await mkdir(options.outDir, { recursive: true });
     }
 
-    // Validate options.version here
-    // We need to do this to get the version specific release info
+    // Validate options.version to get the version specific release info
     releaseInfo = await getReleaseInfo(
       options.version,
       options.cacheDir,
       options.manifestUrl,
     );
+    // Remove leading "v" from version string
+    options.version = releaseInfo.version.slice(1);
 
-    validate(options, releaseInfo);
+    await validate(options, releaseInfo);
 
+    // Variable to store nwDir file path
+    nwDir = `${options.cacheDir}/nwjs${
+      options.flavor === "sdk" ? "-sdk" : ""
+    }-v${options.version}-${options.platform}-${options.arch}`;
+
+    nwCached = await isCached(nwDir);
     // Remove cached NW binary
-    if (options.cache === false &amp;&amp; cached === true) {
+    if (options.cache === false &amp;&amp; nwCached === true) {
       log.debug("Remove cached NW binary");
       await rm(nwDir, { force: true, recursive: true });
     }
     // Download relevant NW.js binaries
-    if (cached === false) {
+    if (nwCached === false) {
       log.debug("Download relevant NW.js binaries");
       await download(
         options.version,
@@ -226,7 +190,7 @@ <h1 class="page-title">Source: nwbuild.js</h1>
     }
   } catch (error) {
     log.error(error);
-    return error;
+    throw error;
   }
 };
 
@@ -248,8 +212,8 @@ <h2><a href="index.html">Home</a></h2
 
     <footer>
       Documentation generated by
-      <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.0</a> on Fri Jan 06
-      2023 17:15:41 GMT-0500 (Eastern Standard Time)
+      <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.0</a> on Sun Feb 05
+      2023 17:00:04 GMT-0500 (Eastern Standard Time)
     </footer>
 
     <script>
diff --git a/package.json b/package.json
index e75db45f8..e37c417e7 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "nw-builder",
-  "version": "4.0.9",
+  "version": "4.0.10",
   "description": "Build NW.js desktop applications for MacOS, Windows and Linux.",
   "keywords": [
     "NW.js",
@@ -21,7 +21,6 @@
   "files": [
     "./src",
     "./LICENSE"
-
   ],
   "homepage": "https://github.com/nwutils/nw-builder",
   "repository": {
@@ -34,8 +33,8 @@
     "docs": "jsdoc ./src/nwbuild.js -d docs",
     "test:unit": "node --experimental-vm-modules node_modules/jest/bin/jest.js",
     "test:e2e": "cd ./test/e2e && node bld.js && node run.js",
-    "demo:cli": "cd ./test/e2e && node cli.js",
-    "demo:nix": "cd ./test/e2e && node nix.js",
+    "demo:cli": "cd ./test/e2e && nwbuild ./nwapp/* ./nwapp/**/* --mode=build --version=latest --flavor=normal --platform=linux --arch=x64 --outDir=./build/cli",
+    "demo:nix": "cd test/e2e && node nix.js",
     "demo:osx": "cd ./test/e2e && node osx.js",
     "demo:win": "cd ./test/e2e && node win.js"
   },
diff --git a/src/bld/package.js b/src/bld/package.js
index d33340733..ddb40a77c 100644
--- a/src/bld/package.js
+++ b/src/bld/package.js
@@ -1,5 +1,5 @@
+import { sep } from "node:path";
 import { cp, rm } from "node:fs/promises";
-import { basename } from "node:path";
 
 import { log } from "../log.js";
 
@@ -34,13 +34,13 @@ const packager = async (
   log.debug(`Copy ${nwDir} files to ${outDir} directory`);
   await cp(nwDir, outDir, { recursive: true });
 
-  for (const file of files) {
+  for (let file of files) {
     log.debug(`Copy ${file} file to ${outDir} directory`);
     await cp(
       file,
       `${outDir}/${
         platform !== "osx" ? "package.nw" : "nwjs.app/Contents/Resources/app.nw"
-      }/${basename(file)}`,
+      }/${file.split(sep).splice(2).join(sep)}`,
       {
         recursive: true,
       },
diff --git a/src/cli.js b/src/cli.js
index 9ccdcdc41..72774a523 100755
--- a/src/cli.js
+++ b/src/cli.js
@@ -37,4 +37,5 @@ const cli = yargs(hideBin(process.argv))
 nwbuild({
   ...cli,
   srcDir: cli._.join(" "),
+  cli: true,
 });
diff --git a/src/nwbuild.js b/src/nwbuild.js
index 5b2884b25..fcb3e7d3a 100644
--- a/src/nwbuild.js
+++ b/src/nwbuild.js
@@ -69,6 +69,7 @@ import { log } from "./log.js";
  * @property {App}                          app                                       Multi platform configuration options
  * @property {boolean}                      [cache=true]                              If true the existing cache is used. Otherwise it removes and redownloads it.
  * @property {boolean}                      [zip=false]                               If true the outDir directory is zipped
+ * @property {boolean}                      [cli=false]                               If true the CLI is used to glob srcDir and parse other options
  */
 
 /**
diff --git a/src/util/options.js b/src/util/options.js
index cd0430f9e..f6433068e 100644
--- a/src/util/options.js
+++ b/src/util/options.js
@@ -16,21 +16,27 @@ export const getOptions = async (opts) => {
   let nwPkg;
   const patterns = opts.srcDir.split(" ");
 
-  for (const pattern of patterns) {
-    let contents = await glob(pattern);
-    files.push(...contents);
-    // Try to find the first instance of the package.json
-    for (const content of contents) {
-      if (basename(content) === "package.json" && nwPkg === undefined) {
-        nwPkg = JSON.parse(await readFile(content));
-      }
+  // If the cli option is not true, then the srcDir glob patterns have not been parsed
+  if (opts.cli !== true) {
+    for (const pattern of patterns) {
+      let contents = await glob(pattern);
+      files.push(...contents);
     }
+  } else {
+    files = [...patterns];
+  }
 
-    if (nwPkg === undefined) {
-      throw new Error("package.json not found in srcDir file glob patterns.");
+  // Try to find the first instance of the package.json
+  for (const file of files) {
+    if (basename(file) === "package.json" && nwPkg === undefined) {
+      nwPkg = JSON.parse(await readFile(file));
     }
   }
 
+  if (nwPkg === undefined) {
+    throw new Error("package.json not found in srcDir file glob patterns.");
+  }
+
   if (files.length === 0) {
     throw new Error(`The globbing pattern ${opts.srcDir} is invalid.`);
   }
diff --git a/test/e2e/cli.js b/test/e2e/cli.js
deleted file mode 100644
index 64c61a0c0..000000000
--- a/test/e2e/cli.js
+++ /dev/null
@@ -1,5 +0,0 @@
-import { exec } from "child_process";
-
-exec(
-  "nwbuild ./nwapp/**/* ./node_modules/**/* --mode=build --version=latest --flavor=normal --platform=win --arch=x64 --outDir=./build",
-);
diff --git a/test/e2e/nwapp/package-lock.json b/test/e2e/nwapp/package-lock.json
new file mode 100644
index 000000000..aa36bff70
--- /dev/null
+++ b/test/e2e/nwapp/package-lock.json
@@ -0,0 +1,591 @@
+{
+  "name": "nwdemo",
+  "version": "0.0.1",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "nwdemo",
+      "version": "0.0.1",
+      "dependencies": {
+        "express": "^4.18.2"
+      }
+    },
+    "node_modules/accepts": {
+      "version": "1.3.8",
+      "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.8.tgz",
+      "integrity": "sha512-PYAthTa2m2VKxuvSD3DPC/Gy+U+sOA1LAuT8mkmRuvw+NACSaeXEQ+NHcVF7rONl6qcaxV3Uuemwawk+7+SJLw==",
+      "dependencies": {
+        "mime-types": "~2.1.34",
+        "negotiator": "0.6.3"
+      },
+      "engines": {
+        "node": ">= 0.6"
+      }
+    },
+    "node_modules/array-flatten": {
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/array-flatten/-/array-flatten-1.1.1.tgz",
+      "integrity": "sha512-PCVAQswWemu6UdxsDFFX/+gVeYqKAod3D3UVm91jHwynguOwAvYPhx8nNlM++NqRcK6CxxpUafjmhIdKiHibqg=="
+    },
+    "node_modules/body-parser": {
+      "version": "1.20.1",
+      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.1.tgz",
+      "integrity": "sha512-jWi7abTbYwajOytWCQc37VulmWiRae5RyTpaCyDcS5/lMdtwSz5lOpDE67srw/HYe35f1z3fDQw+3txg7gNtWw==",
+      "dependencies": {
+        "bytes": "3.1.2",
+        "content-type": "~1.0.4",
+        "debug": "2.6.9",
+        "depd": "2.0.0",
+        "destroy": "1.2.0",
+        "http-errors": "2.0.0",
+        "iconv-lite": "0.4.24",
+        "on-finished": "2.4.1",
+        "qs": "6.11.0",
+        "raw-body": "2.5.1",
+        "type-is": "~1.6.18",
+        "unpipe": "1.0.0"
+      },
+      "engines": {
+        "node": ">= 0.8",
+        "npm": "1.2.8000 || >= 1.4.16"
+      }
+    },
+    "node_modules/bytes": {
+      "version": "3.1.2",
+      "resolved": "https://registry.npmjs.org/bytes/-/bytes-3.1.2.tgz",
+      "integrity": "sha512-/Nf7TyzTx6S3yRJObOAV7956r8cr2+Oj8AC5dt8wSP3BQAoeX58NoHyCU8P8zGkNXStjTSi6fzO6F0pBdcYbEg==",
+      "engines": {
+        "node": ">= 0.8"
+      }
+    },
+    "node_modules/call-bind": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/call-bind/-/call-bind-1.0.2.tgz",
+      "integrity": "sha512-7O+FbCihrB5WGbFYesctwmTKae6rOiIzmz1icreWJ+0aA7LJfuqhEso2T9ncpcFtzMQtzXf2QGGueWJGTYsqrA==",
+      "dependencies": {
+        "function-bind": "^1.1.1",
+        "get-intrinsic": "^1.0.2"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
+    "node_modules/content-disposition": {
+      "version": "0.5.4",
+      "resolved": "https://registry.npmjs.org/content-disposition/-/content-disposition-0.5.4.tgz",
+      "integrity": "sha512-FveZTNuGw04cxlAiWbzi6zTAL/lhehaWbTtgluJh4/E95DqMwTmha3KZN1aAWA8cFIhHzMZUvLevkw5Rqk+tSQ==",
+      "dependencies": {
+        "safe-buffer": "5.2.1"
+      },
+      "engines": {
+        "node": ">= 0.6"
+      }
+    },
+    "node_modules/content-type": {
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/content-type/-/content-type-1.0.5.tgz",
+      "integrity": "sha512-nTjqfcBFEipKdXCv4YDQWCfmcLZKm81ldF0pAopTvyrFGVbcR6P/VAAd5G7N+0tTr8QqiU0tFadD6FK4NtJwOA==",
+      "engines": {
+        "node": ">= 0.6"
+      }
+    },
+    "node_modules/cookie": {
+      "version": "0.5.0",
+      "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.5.0.tgz",
+      "integrity": "sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw==",
+      "engines": {
+        "node": ">= 0.6"
+      }
+    },
+    "node_modules/cookie-signature": {
+      "version": "1.0.6",
+      "resolved": "https://registry.npmjs.org/cookie-signature/-/cookie-signature-1.0.6.tgz",
+      "integrity": "sha512-QADzlaHc8icV8I7vbaJXJwod9HWYp8uCqf1xa4OfNu1T7JVxQIrUgOWtHdNDtPiywmFbiS12VjotIXLrKM3orQ=="
+    },
+    "node_modules/debug": {
+      "version": "2.6.9",
+      "resolved": "https://registry.npmjs.org/debug/-/debug-2.6.9.tgz",
+      "integrity": "sha512-bC7ElrdJaJnPbAP+1EotYvqZsb3ecl5wi6Bfi6BJTUcNowp6cvspg0jXznRTKDjm/E7AdgFBVeAPVMNcKGsHMA==",
+      "dependencies": {
+        "ms": "2.0.0"
+      }
+    },
+    "node_modules/depd": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/depd/-/depd-2.0.0.tgz",
+      "integrity": "sha512-g7nH6P6dyDioJogAAGprGpCtVImJhpPk/roCzdb3fIh61/s/nPsfR6onyMwkCAR/OlC3yBC0lESvUoQEAssIrw==",
+      "engines": {
+        "node": ">= 0.8"
+      }
+    },
+    "node_modules/destroy": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/destroy/-/destroy-1.2.0.tgz",
+      "integrity": "sha512-2sJGJTaXIIaR1w4iJSNoN0hnMY7Gpc/n8D4qSCJw8QqFWXf7cuAgnEHxBpweaVcPevC2l3KpjYCx3NypQQgaJg==",
+      "engines": {
+        "node": ">= 0.8",
+        "npm": "1.2.8000 || >= 1.4.16"
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diff --git a/test/e2e/nwapp/package.json b/test/e2e/nwapp/package.json
index 595b363bf..b82ec2c31 100644
--- a/test/e2e/nwapp/package.json
+++ b/test/e2e/nwapp/package.json
@@ -2,5 +2,8 @@
   "name": "nwdemo",
   "version": "0.0.1",
   "main": "index.html",
-  "author": "ABC Corp"
+  "author": "ABC Corp",
+  "dependencies": {
+    "express": "^4.18.2"
+  }
 }