diff --git a/lib/_update_javascripts.js b/lib/_update_javascripts.js
index 7ff0f359d1..cc29ca5ad4 100644
--- a/lib/_update_javascripts.js
+++ b/lib/_update_javascripts.js
@@ -1,43 +1,13 @@
 const fs = require('fs').promises
-const https = require('https')
 const path = require('path')
 
-const { projectDir, packageDir } = require('./path-utils')
+const { projectDir } = require('./path-utils')
+const { getProjectVersion, fetchOriginal } = require('./update-utils')
 
-async function getProjectVersion () {
-  return (await fs.readFile(path.join(projectDir, 'VERSION.txt'), 'utf8')).trim()
-}
-
-async function fetchOriginal (version, filePath) {
-  const remoteUrl = `https://raw.githubusercontent.com/alphagov/govuk-prototype-kit/v${version}/${filePath}`
-
-  let data = ''
-  return new Promise((resolve, reject) => {
-    https.get(remoteUrl, (response) => {
-      let error
-
-      if (response.statusCode !== 200) {
-        error = new Error(`could not fetch ${remoteUrl}: status code ${response.statusCode}`)
-        Object.assign(error, response)
-        response.resume()
-        reject(error)
-      }
-
-      response.setEncoding('utf8')
-
-      response.on('data', (chunk) => {
-        data += chunk
-      })
-
-      response.on('end', () => {
-        resolve(data)
-      })
-    })
-  })
-}
+const updateDir = path.join(projectDir, 'update')
 
 async function removeKitJsFromApplicationJs () {
-  const userVersion = getProjectVersion()
+  const userVersion = await getProjectVersion()
 
   // If the user already has version 13 or greater of the kit installed then
   // their application.js file is all their code and we don't don't want to
@@ -52,17 +22,17 @@ async function removeKitJsFromApplicationJs () {
 
   // If the user hasn't changed their application.js file we can just replace it completely
   if (original === theirs) {
-    return fs.copyFile(path.join(packageDir, 'lib', assetPath), path.join(projectDir, 'app', assetPath))
+    return fs.copyFile(path.join(updateDir, 'app', assetPath), path.join(projectDir, 'app', assetPath))
   }
 
   // Otherwise, if the original code is contained as-is in their file, we can
   // remove the shared lines, and add our hints
   if (theirs.includes(original)) {
-    const ours = await fs.readFile(path.resolve(packageDir, 'app', assetPath), 'utf8')
+    const ours = await fs.readFile(path.resolve(updateDir, 'app', assetPath), 'utf8')
 
     let merged
-    merged = theirs.replace(original, '\n')
-    merged = ours + '\n' + merged
+    merged = theirs.replace(original, '')
+    merged = ours + merged
     return fs.writeFile(path.resolve(projectDir, 'app', assetPath), merged, 'utf8')
   }
 
@@ -88,6 +58,11 @@ async function main () {
   await removeKitJsFromApplicationJs()
 }
 
+module.exports = {
+  /* exported for tests only */
+  removeKitJsFromApplicationJs
+}
+
 if (require.main === module) {
   main()
 }
diff --git a/lib/_update_javascripts.test.js b/lib/_update_javascripts.test.js
new file mode 100644
index 0000000000..42b53f9ff0
--- /dev/null
+++ b/lib/_update_javascripts.test.js
@@ -0,0 +1,103 @@
+/* eslint-env jest */
+
+const fs = require('fs').promises
+const path = require('path')
+
+const updateUtils = require('./update-utils')
+updateUtils.getProjectVersion = jest.fn()
+updateUtils.fetchOriginal = jest.fn()
+
+const updatejs = require('./_update_javascripts')
+
+const oldApplicationJs = `/* global $ */
+
+// Warn about using the kit in production
+if (window.console && window.console.info) {
+  window.console.info('GOV.UK Prototype Kit - do not use for production')
+}
+
+$(document).ready(function () {
+  window.GOVUKFrontend.initAll()
+})
+`
+
+const newApplicationJs = `// Add extra JavaScript here
+
+ready(() => {
+  // Add JavaScript that needs to be run when the page is loaded
+})
+`
+
+describe('removeKitJsFromApplicationJs', () => {
+  afterEach(() => {
+    jest.restoreAllMocks()
+  })
+
+  beforeEach(() => {
+    jest.spyOn(updateUtils, 'getProjectVersion').mockImplementation(
+      async () => '12.1.1'
+    )
+
+    jest.spyOn(updateUtils, 'fetchOriginal').mockImplementation(
+      async () => oldApplicationJs
+    )
+  })
+
+  it('replaces application.js if the user has not updated it', async () => {
+    jest.spyOn(fs, 'readFile').mockImplementationOnce(
+      async () => oldApplicationJs
+    )
+
+    const mockCopyFile = jest.spyOn(fs, 'copyFile').mockImplementation(
+      async () => {}
+    )
+
+    await updatejs.removeKitJsFromApplicationJs()
+
+    expect(mockCopyFile).toHaveBeenCalledWith(
+      expect.stringContaining(path.join('update', 'app', 'assets', 'javascripts', 'application.js')),
+      expect.stringContaining(path.join('app', 'assets', 'javascripts', 'application.js'))
+    )
+  })
+
+  it('rewrites application.js if the user has added lines to the bottom of the file', async () => {
+    // theirs
+    jest.spyOn(fs, 'readFile').mockImplementationOnce(
+      async () => oldApplicationJs + '\ncallMyCode()\n'
+    )
+    // ours
+    jest.spyOn(fs, 'readFile').mockImplementationOnce(
+      async () => newApplicationJs
+    )
+
+    const mockWriteFile = jest.spyOn(fs, 'writeFile').mockImplementation(
+      async () => {}
+    )
+
+    await updatejs.removeKitJsFromApplicationJs()
+
+    expect(mockWriteFile).toHaveBeenCalledWith(
+      expect.stringContaining(path.join('app', 'assets', 'javascripts', 'application.js')),
+      newApplicationJs + '\ncallMyCode()\n',
+      'utf8'
+
+  it('does not touch application.js if the user has rewritten it a lot', async () => {
+    // theirs
+    jest.spyOn(fs, 'readFile').mockImplementationOnce(
+      async () => 'justMyCode()\n'
+    )
+
+    const mockWriteFile = jest.spyOn(fs, 'writeFile').mockImplementation(
+      async () => {}
+    )
+
+    const mockCopyFile = jest.spyOn(fs, 'copyFile').mockImplementation(
+      async () => {}
+    )
+
+    await updatejs.removeKitJsFromApplicationJs()
+
+    expect(mockWriteFile).not.toHaveBeenCalled()
+    expect(mockCopyFile).not.toHaveBeenCalled()
+  })
+})
diff --git a/lib/update-utils.js b/lib/update-utils.js
new file mode 100644
index 0000000000..bac3037100
--- /dev/null
+++ b/lib/update-utils.js
@@ -0,0 +1,42 @@
+const fs = require('fs').promises
+const https = require('https')
+const path = require('path')
+
+const { projectDir } = require('./path-utils')
+
+async function getProjectVersion () {
+  return (await fs.readFile(path.join(projectDir, 'VERSION.txt'), 'utf8')).trim()
+}
+
+async function fetchOriginal (version, filePath) {
+  const remoteUrl = `https://raw.githubusercontent.com/alphagov/govuk-prototype-kit/v${version}/${filePath}`
+
+  let data = ''
+  return new Promise((resolve, reject) => {
+    https.get(remoteUrl, (response) => {
+      let error
+
+      if (response.statusCode !== 200) {
+        error = new Error(`could not fetch ${remoteUrl}: status code ${response.statusCode}`)
+        Object.assign(error, response)
+        response.resume()
+        reject(error)
+      }
+
+      response.setEncoding('utf8')
+
+      response.on('data', (chunk) => {
+        data += chunk
+      })
+
+      response.on('end', () => {
+        resolve(data)
+      })
+    })
+  })
+}
+
+module.exports = {
+  fetchOriginal,
+  getProjectVersion
+}
diff --git a/lib/update-utils.test.js b/lib/update-utils.test.js
new file mode 100644
index 0000000000..9c0e1b96c2
--- /dev/null
+++ b/lib/update-utils.test.js
@@ -0,0 +1,48 @@
+/* eslint-env jest */
+
+const fs = require('fs').promises
+const https = require('https')
+const stream = require('stream')
+
+const { fetchOriginal, getProjectVersion } = require('./update-utils.js')
+
+afterEach(() => {
+  jest.restoreAllMocks()
+})
+
+describe('fetchOriginal', () => {
+  it('gets the contents of a file as of version from GitHub', async () => {
+    const mockHttpsGet = jest.spyOn(https, 'get').mockImplementation((url, callback) => {
+      const response = new stream.PassThrough()
+      response.statusCode = 200
+
+      callback(response)
+
+      response.write('foo\n')
+      response.write('bar\n')
+      response.end()
+    })
+
+    await expect(fetchOriginal('99.99.99', 'app/views/foo.html')).resolves.toEqual(
+      'foo\nbar\n'
+    )
+    expect(mockHttpsGet).toHaveBeenCalledWith(
+      'https://raw.githubusercontent.com/alphagov/govuk-prototype-kit/v99.99.99/app/views/foo.html',
+      expect.anything()
+    )
+  })
+})
+
+describe('getProjectVersion', () => {
+  it('reads the VERSION.txt file to get the version number', async () => {
+    const mockReadFile = jest.spyOn(fs, 'readFile').mockImplementation(
+      async () => '99.99.99\n'
+    )
+
+    await expect(getProjectVersion()).resolves.toEqual('99.99.99')
+    expect(mockReadFile).toHaveBeenCalledWith(
+      expect.stringMatching(/.*\/VERSION.txt$/),
+      'utf8'
+    )
+  })
+})