Nextcloud: Some files have not passed the integrity check

What the message looks like

There were problems with the code integrity check. More information…
Results:
- core
  - INVALID_HASH
    - core/js/mimetypelist.js
  - EXTRA_FILE
    - core/old-backup.php

Common causes

• Files were left over or mixed after a manual update, for example an old folder copied over a new one.
• A core or app file was edited by hand, or a backup, patch or .orig file was put into the program folder.
• An upload or unzip was incomplete, so files are missing (MISSING_FILE) or damaged (INVALID_HASH).
• An app that did not come from the App Store, or a custom theme placed in the wrong folder, is reported as extra.

Check

1. Check the core files
   sudo -u www-data php occ integrity:check-coreCopy
2. Check one app
   sudo -u www-data php occ integrity:check-app calendarCopy
3. Which version is installed?
   sudo -u www-data php occ statusCopy
4. Files changed in the last days
   find /var/www/nextcloud -maxdepth 2 -type f -mtime -3 -not -path '*/data/*' | head -n 20Copy

Fix

• Read the result: INVALID_HASH means the file was changed, MISSING_FILE means it is gone, EXTRA_FILE means it does not belong there.
• Download the archive of exactly your installed version from the official source, verify its checksum, and copy the reported files back from it.
• Move EXTRA_FILE entries out of the program folder, for example to a backup folder outside the web root.
• Put custom themes and apps in themes/ and custom_apps/, not into core folders. Use updater/updater.phar or the web updater for future updates.
• Run occ integrity:check-core again, then press the rescan button in the admin overview.

FAQ

Can I ignore this warning?

It can point to a broken or tampered installation, so do not leave it. If the list holds only a file you changed on purpose, document it. Otherwise restore the original so updates and support stay predictable.

Does the check touch my data directory?

No. It only looks at the program files, the shipped apps and the signed apps. Your data folder is not compared.