Below is the diff I have collected based on the following criteria:

Diff is master v/s stable10 apps/encryption folder
Ignore files with only copyright year diff
Ignore info.xml
Ignored tests

The diff of the files are as shown below
master v/s stable10

Excluding files with Copyright year diff and info.xml

appinfo/Migrations/Version20170913113840.php

5c5
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
35c35
<               if (\version_compare('10.0.3', $installedVersion, '>=') === true) {
---
>               if (version_compare('10.0.3', $installedVersion, '>=') === true) {
47a48,49
> 
>

js/settings-admin.js

106,107d105
<                                       $("#encryptionRecoveryPassword").val("");
<                                       $("#repeatEncryptionRecoveryPassword").val("");

lib/Command/MigrateKeys.php

6c6
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
61a62
> 
100,101c101,102
<                       foreach ($this->userManager->getBackends() as $backend) {
<                               $name = \get_class($backend);
---
>                       foreach($this->userManager->getBackends() as $backend) {
>                               $name = get_class($backend);
118c119
<                               } while (\count($users) >= $limit);
---
>                               } while(count($users) >= $limit);
122a124
>

lib/Command/RecreateMasterKey.php

5c5
< * @copyright Copyright (c) 2017, ownCloud GmbH
---
> * @copyright Copyright (c) 2018, ownCloud GmbH
21a22
> 
130a132
> 
172a175
> 
182a186
> 
198a203
> 
240c245
<               $this->decryptAll->decryptAll($input, $output);
---
>               $this->decryptAll->decryptAll($input,$output);
258a264
>

lib/Command/SelectEncryptionType.php

5c5
< * @copyright Copyright (c) 2017, ownCloud GmbH
---
> * @copyright Copyright (c) 2018, ownCloud GmbH
21a22
> 
52a54
> 
81c83
<               if ($this->config->getAppValue('core', 'encryption_enabled', 'no') === 'no') {
---
>               if($this->config->getAppValue('core', 'encryption_enabled', 'no') === 'no') {
90c92
<               $userKeysNotEnabled = ($this->config->getAppValue('encryption', 'userSpecificKey', '') === '');
---
>               $userKeysNotEnabled = ($this->config->getAppValue('encryption','userSpecificKey', '') === '');
93,94c95,96
<               if (!$freshInstallation) {
<                       if (!$masterKeyNotEnabled) {
---
>               if(!$freshInstallation) {
>                       if(!$masterKeyNotEnabled) {
102c104
<               if ($encryptionType === "masterkey") {
---
>               if($encryptionType === "masterkey") {
120a123
> 
122a126
>

lib/Controller/RecoveryController.php

7c7
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
25a26
> 
122c123
<                       return new DataResponse(['data' => ['message' => $errorMessage]], Http::STATUS_BAD_REQUEST);
---
>                       return new DataResponse (['data' => ['message' => $errorMessage]], Http::STATUS_BAD_REQUEST);
161a163
> 
179a182
> 
187a191
>

lib/Controller/SettingsController.php

6c6
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
97a98
> 
143c144
<                               ['message' => (string)$this->l->t('Private key password successfully updated.')]
---
>                               ['message' => (string) $this->l->t('Private key password successfully updated.')]
147c148
<                               ['message' => (string)$errorMessage],
---
>                               ['message' => (string) $errorMessage],
150a152
>

lib/Controller/StatusController.php

6c6
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
22a23
> 
24a26
> 
59a62
> 
62c65
<               switch ($this->session->getStatus()) {
---
>               switch( $this->session->getStatus()) {
93a97
>

lib/Crypto/DecryptAll.php

5c5
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
21a22
> 
23a25
> 
133c135
<                       if (!$input->hasOption('method') && !\in_array($input->getOption('method'), ['recovery', 'password'])) {
---
>                       if(!$input->hasOption('method') && !in_array($input->getOption('method'),['recovery', 'password'])) {
200c202,203
<                                       }
---
>                               }
>

lib/Crypto/EncryptAll.php

7c7
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
23a24
> 
128a130
> 
135c137
<               $this->output->writeln(\str_pad('', \strlen($headline), '='));
---
>               $this->output->writeln(str_pad('', strlen($headline), '='));
178c180
<               foreach ($this->userManager->getBackends() as $backend) {
---
>               foreach($this->userManager->getBackends() as $backend) {
197c199
<                       } while (\count($users) >= $limit);
---
>                       } while(count($users) >= $limit);
212c214
<               $numberOfUsers = \count($this->userPasswords);
---
>               $numberOfUsers = count($this->userPasswords);
224a227
> 
234c237
<               foreach ($this->userManager->getBackends() as $backend) {
---
>               foreach($this->userManager->getBackends() as $backend) {
245c248
<                       } while (\count($users) >= $limit);
---
>                       } while(count($users) >= $limit);
256a260
> 
259c263
<               $directories[] = '/' . $uid . '/files';
---
>               $directories[] =  '/' . $uid . '/files';
261c265
<               while ($root = \array_pop($directories)) {
---
>               while($root = array_pop($directories)) {
275c279
<                                       if ($this->encryptFile($path) === false) {
---
>                                       if($this->encryptFile($path) === false) {
290a295
> 
292c297
<               $target = $path . '.encrypted.' . \time() . '.part';
---
>               $target = $path . '.encrypted.' . $this->getTimeStamp() . '.part';
296c301
<                       if ($version > 0) {
---
>                       if ($version > 0)  {
361c366
<                       \fputcsv($fp, $pwd);
---
>                       fputcsv($fp, $pwd);
363c368
<               \fclose($fp);
---
>               fclose($fp);
384a390,398
>        * get current timestamp
>        *
>        * @return int
>        */
>       protected function getTimeStamp() {
>               return \time();
>       }
> 
>       /**
403c417
<               $progress = new ProgressBar($this->output, \count($this->userPasswords));
---
>               $progress = new ProgressBar($this->output, count($this->userPasswords));
453a468
> 
462a478
> 
464c480
<               $html->assign('password', $password);
---
>               $html->assign ('password', $password);
468c484
<               $plainText->assign('password', $password);
---
>               $plainText->assign ('password', $password);
472a489
>

lib/Crypto/Encryption.php

10c10
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
28a29
> 
42a44
> 
107a110
> 
165c168
<        *                                              This is helpful for revision increment during move operation between storage.
---
>        *                                                                              This is helpful for revision increment during move operation between storage.
211c214
<                       if (Scanner::isPartialFile($path)) {
---
>                       if(Scanner::isPartialFile($path)) {
301a305
> 
306c310
<               while (\strlen($data) > 0) {
---
>               while (strlen($data) > 0) {
310c314
<                       $remainingLength = \strlen($data);
---
>                       $remainingLength = strlen($data);
327a332
> 
331c336
<                               $chunk = \substr($data, 0, $this->unencryptedBlockSizeSigned);
---
>                               $chunk = substr($data, 0, $this->unencryptedBlockSizeSigned);
338c343,344
<                               $data = \substr($data, $this->unencryptedBlockSizeSigned);
---
>                               $data = substr($data, $this->unencryptedBlockSizeSigned);
> 
339a346
> 
373a381
> 
384a393
> 
404a414
> 
428,429c438,439
<               $parts = \explode('/', $path);
<               if (\count($parts) < 4) {
---
>               $parts = explode('/', $path);
>               if (count($parts) < 4) {
512a523
> 
519c530
<               $parts = \explode('/', $path);
---
>               $parts = explode('/', $path);
521,523c532,534
<                       $realPath = '/' . $parts[1] . '/files/' . \implode('/', \array_slice($parts, 3));
<                       $length = \strrpos($realPath, '.');
<                       $realPath = \substr($realPath, 0, $length);
---
>                       $realPath = '/' . $parts[1] . '/files/' . implode('/', array_slice($parts, 3));
>                       $length = strrpos($realPath, '.');
>                       $realPath = substr($realPath, 0, $length);
537,539c548,550
<               if (\pathinfo($path, PATHINFO_EXTENSION) === 'part') {
<                       $pos = \strrpos($path, '.', -6);
<                       $path = \substr($path, 0, $pos);
---
>               if (pathinfo($path, PATHINFO_EXTENSION) === 'part') {
>                       $pos = strrpos($path, '.', -6);
>                       $path = substr($path, 0, $pos);

lib/Exceptions/PrivateKeyMissingException.php

7c7
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
34c34
<               if (empty($userId)) {
---
>               if(empty($userId)) {
38a39
>

lib/Exceptions/PublicKeyMissingException.php

5c5
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
31c31
<               if (empty($userId)) {
---
>               if(empty($userId)) {
35a36
>

lib/HookManager.php

6c6
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
24a25
> 
27a29
> 
36c38
<               if (\is_array($instances)) {
---
>               if (is_array($instances)) {
42a45
> 
57a61
> 
58a63
>

lib/Migration.php

8c8
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
26a27
> 
32a34
> 
92c94
<                       $users = \OC::$server->getUserManager()->search('', $limit, $offset);
---
>                       $users = \OCP\User::getUsers('', $limit, $offset);
94c96
<                               $this->reorganizeFolderStructureForUser($user->getUID());
---
>                               $this->reorganizeFolderStructureForUser($user);
97c99
<               } while (\count($users) >= $limit);
---
>               } while (count($users) >= $limit);
103a106
> 
118a122
> 
171c175
<                       if ($row['configkey'] !== 'installed_version') {
---
>                       if ($row['configkey'] !== 'installed_version' ) {
194c198
<               $backupDir = 'encryption_migration_backup_' . \date("Y-m-d_H-i-s");
---
>               $backupDir = 'encryption_migration_backup_' . date("Y-m-d_H-i-s");
208c212
<                       $backupDir = $user . '/encryption_migration_backup_' . \date("Y-m-d_H-i-s");
---
>                       $backupDir = $user . '/encryption_migration_backup_' . date("Y-m-d_H-i-s");
221,224c225,228
<               $this->createPathForKeys('/files_encryption/' . $this->moduleId);
<               if (\is_resource($dh)) {
<                       while (($privateKey = \readdir($dh)) !== false) {
<                               if (!\OC\Files\Filesystem::isIgnoredDir($privateKey)) {
---
>               $this->createPathForKeys('/files_encryption/' . $this->moduleId );
>               if (is_resource($dh)) {
>                       while (($privateKey = readdir($dh)) !== false) {
>                               if (!\OC\Files\Filesystem::isIgnoredDir($privateKey) ) {
231c235
<                       \closedir($dh);
---
>                       closedir($dh);
241c245
<               $publicKey = \substr($privateKey, 0, \strrpos($privateKey, '.privateKey')) . '.publicKey';
---
>               $publicKey = substr($privateKey,0 , strrpos($privateKey, '.privateKey')) . '.publicKey';
254c258
<                       $this->createPathForKeys(\dirname($newPrivateKey));
---
>                       $this->createPathForKeys(dirname($newPrivateKey));
268c272
<                       $this->createPathForKeys(\dirname($newPublicKey));
---
>                       $this->createPathForKeys(dirname($newPublicKey));
280a285
> 
288,289c293,294
<               if (\is_resource($dh)) {
<                       while (($file = \readdir($dh)) !== false) {
---
>               if (is_resource($dh)) {
>                       while (($file = readdir($dh)) !== false) {
296c301
<                                                       $this->createPathForKeys(\dirname($target));
---
>                                                       $this->createPathForKeys(dirname($target));
307c312
<                       \closedir($dh);
---
>                       closedir($dh);
333c338
<                       $filePath = \substr($keyPath, \strlen('/files_trashbin/keys/'));
---
>                       $filePath = substr($keyPath, strlen('/files_trashbin/keys/'));
336c341
<                       $filePath = \substr($keyPath, \strlen('/files_encryption/keys/'));
---
>                       $filePath = substr($keyPath, strlen('/files_encryption/keys/'));
346c351
<                               if (\strpos($normalized, $normalizedMountPoint) === 0) {
---
>                               if (strpos($normalized, $normalizedMountPoint) === 0)
348d352
<                               }
350,352c354
<               } elseif ($trash === false && $this->view->file_exists('/' . $user . '/files/' . $filePath)) {
<                       return $targetDir;
<               } elseif ($trash === true && $this->view->file_exists('/' . $user . '/files_trashbin/' . $filePath)) {
---
>               } else if ($trash === false && $this->view->file_exists('/' . $user. '/files/' . $filePath)) {
354c356,358
<               }
---
>               } else if ($trash === true && $this->view->file_exists('/' . $user. '/files_trashbin/' . $filePath)) {
>                               return $targetDir;
>                       }
376c380
<                       $sub_dirs = \explode('/', $path);
---
>                       $sub_dirs = explode('/', $path);

lib/Session.php

7c7
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
62,63c62,63
<               if ($status === null) {
<                       if (\OC::$server->getAppConfig()->getValue('encryption', 'useMasterKey', '0') !== '0'
---
>               if (is_null($status)) {
>                       if(\OC::$server->getAppConfig()->getValue('encryption', 'useMasterKey', '0') !== '0'
80c80
<               if ($key === null) {
---
>               if (is_null($key)) {
93c93
<               if ($key === null) {
---
>               if (is_null($key)) {
141c141
<               if (($uid === null) && $this->decryptAllModeActivated()) {
---
>               if (is_null($uid) && $this->decryptAllModeActivated()) {
143c143
<               } elseif ($uid === null) {
---
>               } elseif (is_null($uid)) {
158c158
<               if (($privateKey === null) && $this->decryptAllModeActivated()) {
---
>               if (is_null($privateKey) && $this->decryptAllModeActivated()) {
160c160
<               } elseif ($privateKey === null) {
---
>               } elseif (is_null($privateKey)) {
177a178
>

lib/Util.php

7c7
<  * @copyright Copyright (c) 2017, ownCloud GmbH
---
>  * @copyright Copyright (c) 2018, ownCloud GmbH
23a24
> 
25a27
> 
175,176c177,178
<               $parts = \explode('/', $path, 3);
<               if (\count($parts) > 1) {
---
>               $parts = explode('/', $path, 3);
>               if (count($parts) > 1) {
181a184
> 
196a200
>

templates/altmail.php

6c6
< if (isset($_['expiration'])) {
---
> if ( isset($_['expiration']) ) {
16c16
< <?php print_unescaped("\n" . $theme->getBaseUrl());
---
> <?php print_unescaped("\n".$theme->getBaseUrl());

templates/mail.php

9,10c9,10
<                                       <td bgcolor="<?php p($theme->getMailHeaderColor()); ?>" width="20px">&nbsp;</td>
<                                       <td bgcolor="<?php p($theme->getMailHeaderColor()); ?>">
---
>                                       <td bgcolor="<?php p($theme->getMailHeaderColor());?>" width="20px">&nbsp;</td>
>                                       <td bgcolor="<?php p($theme->getMailHeaderColor());?>">
31c31
<                                               <br><a href="<?php p($theme->getBaseUrl()); ?>"><?php p($theme->getBaseUrl()); ?></a>
---
>                                               <br><a href="<?php p($theme->getBaseUrl()); ?>"><?php p($theme->getBaseUrl());?></a>

templates/settings-admin.php

9c9
<       <?php if (!$_["initStatus"] and (\OC::$server->getAppConfig()->getValue('encryption', 'useMasterKey', '0') !== '0'
---
>       <?php if(!$_["initStatus"] and (\OC::$server->getAppConfig()->getValue('encryption', 'useMasterKey', '0') !== '0'
17c17
<                       if ($masterKey !== '0') {
---
>                       if($masterKey !== '0') {
20c20
<                               if ($userSpecificKey !== "") {
---
>                               if($userSpecificKey !== "") {
32c32
<                       <button id="select-mode" type="button" class="hidden"><?php p($l->t("Permanently select this mode")); ?></button>
---
>                       <button id="select-mode" type="button" class="hidden"><?php p($l->t("Permanently select this mode"));?></button>
34,35c34,35
<                       <div id="masterKeyVal" data-master-key="<?php echo \OC::$server->getAppConfig()->getValue("encryption", "useMasterKey", ""); ?>"></div>
<                       <div id="userSpecificKey" data-user-specific-key="<?php echo \OC::$server->getAppConfig()->getValue("encryption", "userSpecificKey", ""); ?>"></div>
---
>                       <div id="masterKeyVal" data-master-key="<?php echo \OC::$server->getAppConfig()->getValue("encryption", "useMasterKey", "");?>"></div>
>                       <div id="userSpecificKey" data-user-specific-key="<?php echo \OC::$server->getAppConfig()->getValue("encryption", "userSpecificKey", "");?>"></div>
41,45c41,43
<                                  value="1" <?php if ($_['encryptHomeStorage']) {
<                               print_unescaped('checked="checked"');
<                       } ?> />
<                       <label for="encryptHomeStorage"><?php p($l->t('Encrypt the home storage')); ?></label></br>
<                       <em><?php p($l->t("Enabling this option encrypts all files stored on the main storage, otherwise only files on external storage will be encrypted")); ?></em>
---
>                                  value="1" <?php if ($_['encryptHomeStorage']) print_unescaped('checked="checked"'); ?> />
>                       <label for="encryptHomeStorage"><?php p($l->t('Encrypt the home storage'));?></label></br>
>                       <em><?php p( $l->t( "Enabling this option encrypts all files stored on the main storage, otherwise only files on external storage will be encrypted" ) ); ?></em>
48c46
<               <?php if ($_['masterKeyEnabled'] === false): ?>
---
>               <?php if($_['masterKeyEnabled'] === false): ?>
50c48
<                               <?php $_["recoveryEnabled"] === '0' ? p($l->t("Enable recovery key")) : p($l->t("Disable recovery key")); ?>
---
>                               <?php $_["recoveryEnabled"] === '0' ?  p($l->t("Enable recovery key")) : p($l->t("Disable recovery key")); ?>
69c67
<                                          value="<?php $_["recoveryEnabled"] === '0' ? p($l->t("Enable recovery key")) : p($l->t("Disable recovery key")); ?>"/>
---
>                                          value="<?php $_["recoveryEnabled"] === '0' ?  p($l->t("Enable recovery key")) : p($l->t("Disable recovery key")); ?>"/>
73,75c71
<                       <p name="changeRecoveryPasswordBlock" id="encryptionChangeRecoveryKey" <?php if ($_['recoveryEnabled'] === '0') {
<                               print_unescaped('class="hidden"');
<                       } ?>>
---
>                       <p name="changeRecoveryPasswordBlock" id="encryptionChangeRecoveryKey" <?php if($_['recoveryEnabled'] === '0') print_unescaped('class="hidden"');?>>

templates/settings-personal.php

9c9
<       <?php if ($_["initialized"] === \OCA\Encryption\Session::NOT_INITIALIZED): ?>
---
>       <?php if ($_["initialized"] === \OCA\Encryption\Session::NOT_INITIALIZED ): ?>
13c13
<       <?php elseif ($_["initialized"] === \OCA\Encryption\Session::INIT_EXECUTED): ?>
---
>       <?php elseif ( $_["initialized"] === \OCA\Encryption\Session::INIT_EXECUTED ): ?>
17c17
<                               <em><?php p($l->t("Your private key password no longer matches your log-in password.")); ?></em>
---
>                               <em><?php p( $l->t( "Your private key password no longer matches your log-in password." ) ); ?></em>
20,22c20,22
<                       <?php p($l->t("Set your old private key password to your current log-in password:")); ?>
<                       <?php if ($_["recoveryEnabledForUser"]):
<                                       p($l->t(" If you don't remember your old password you can ask your administrator to recover your files."));
---
>                       <?php p( $l->t( "Set your old private key password to your current log-in password:" ) ); ?>
>                       <?php if (  $_["recoveryEnabledForUser"] ):
>                                       p( $l->t( " If you don't remember your old password you can ask your administrator to recover your files." ) );
29c29
<                       <label for="oldPrivateKeyPassword"><?php p($l->t("Old log-in password")); ?></label>
---
>                       <label for="oldPrivateKeyPassword"><?php p($l->t( "Old log-in password" )); ?></label>
35c35
<                       <label for="newRecoveryPassword"><?php p($l->t("Current log-in password")); ?></label>
---
>                       <label for="newRecoveryPassword"><?php p($l->t( "Current log-in password" )); ?></label>
40c40
<                               disabled><?php p($l->t("Update Private Key Password")); ?>
---
>                               disabled><?php p($l->t( "Update Private Key Password" )); ?>
45c45
<       <?php elseif ($_["recoveryEnabled"] && $_["privateKeySet"] && $_["initialized"] === \OCA\Encryption\Session::INIT_SUCCESSFUL): ?>
---
>       <?php elseif ( $_["recoveryEnabled"] && $_["privateKeySet"] &&  $_["initialized"] === \OCA\Encryption\Session::INIT_SUCCESSFUL ): ?>
48c48
<                       <label for="userEnableRecovery"><?php p($l->t("Enable password recovery:")); ?></label>
---
>                       <label for="userEnableRecovery"><?php p( $l->t( "Enable password recovery:" ) ); ?></label>
51c51
<                       <em><?php p($l->t("Enabling this option will allow you to reobtain access to your encrypted files in case of password loss")); ?></em>
---
>                       <em><?php p( $l->t( "Enabling this option will allow you to reobtain access to your encrypted files in case of password loss" ) ); ?></em>
58,59c58,59
<                       <?php echo($_["recoveryEnabledForUser"] ? 'checked="checked"' : ''); ?> />
<                       <label for="userEnableRecoveryCheckbox"><?php p($l->t("Enabled")); ?></label>
---
>                       <?php echo ( $_["recoveryEnabledForUser"] ? 'checked="checked"' : '' ); ?> />
>                       <label for="userEnableRecoveryCheckbox"><?php p( $l->t( "Enabled" ) ); ?></label>
67,68c67,68
<                       <?php echo($_["recoveryEnabledForUser"] === false ? 'checked="checked"' : ''); ?> />
<                       <label for="userDisableRecoveryCheckbox"><?php p($l->t("Disabled")); ?></label>
---
>                       <?php echo ( $_["recoveryEnabledForUser"] === false ? 'checked="checked"' : '' ); ?> />
>                       <label for="userDisableRecoveryCheckbox"><?php p( $l->t( "Disabled" ) ); ?></label>

In my next comment I will exclude the files which have diff's like space or adding \ before functions.

Check code alignment #118

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