XF 2.0 How to fix a messed up upgrade?

During an upgrade I get this message:

Upgrade system
There are at least 5 file(s) that do not appear to have the expected contents. Reupload the XenForo files and refresh this page. Only continue if you are sure all files have been uploaded properly.
The following warnings were detected when verifying that your server can run XenForo:
  • Your server has disabled a core PHP function exec via the disable_functions directive in php.ini. This may cause unexpected problems in XenForo.
  • Your server has disabled a core PHP function proc_open via the disable_functions directive in php.ini. This may cause unexpected problems in XenForo.
  • Your server has disabled a core PHP function popen via the disable_functions directive in php.ini. This may cause unexpected problems in XenForo.
These will not prevent you from using XenForo, but they should be resolved if possible to ensure optimal functioning. However, you may still continue with the upgrade.
Click the button below to begin the upgrade to 2.0.11.

I have uploaded the files several times, if I continue with the upgrade I get this message:

An exception occurred: [Error] Class 'XF\AddOn\DataType\PermissionInterfaceGroup' not found in src/XF/AddOn/DataManager.php on line 149
  1. XF\AddOn\DataManager->getDataTypeHandler() in src/XF/Job/AddOnData.php at line 61
  2. XF\Job\AddOnData->run() in src/XF/Job/Atomic.php at line 38
  3. XF\Job\Atomic->run() in src/XF/Job/Manager.php at line 241
  4. XF\Job\Manager->runJobInternal() in src/XF/Job/Manager.php at line 187
  5. XF\Job\Manager->runJobEntry() in src/XF/Job/Manager.php at line 138
  6. XF\Job\Manager->runUnique() in src/XF/Install/Controller/AbstractController.php at line 24
  7. XF\Install\Controller\AbstractController->manualJobRunner() in src/XF/Install/Controller/Upgrade.php at line 251
  8. XF\Install\Controller\Upgrade->actionRunJob() in src/XF/Mvc/Dispatcher.php at line 249
  9. XF\Mvc\Dispatcher->dispatchClass() in src/XF/Mvc/Dispatcher.php at line 88
  10. XF\Mvc\Dispatcher->dispatchLoop() in src/XF/Mvc/Dispatcher.php at line 41
  11. XF\Mvc\Dispatcher->run() in src/XF/App.php at line 1931
  12. XF\App->run() in src/XF.php at line 329
  13. XF::runApp() in install/index.php at line 14

When I try to view the forum or admin it just says
The site is currently being upgraded. Please check back later.

Any suggestions how to fix this issue?
 
Hello,

You need to ask your host provider for this :
  • Your server has disabled a core PHP function exec via the disable_functions directive in php.ini. This may cause unexpected problems in XenForo.
  • Your server has disabled a core PHP function proc_open via the disable_functions directive in php.ini. This may cause unexpected problems in XenForo.
  • Your server has disabled a core PHP function popen via the disable_functions directive in php.ini. This may cause unexpected problems in XenForo

Regards, SyTry
 
The fundamental issue appears to be missing or corrupt files.

Download the package again from your customer account and upload the files again.

I recommend using cPanel and uploading the zip archive, then extracting directly on the server.
Or SSH, if you know how to use that.
 
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