Error: User warning: The following module is missing from the file system: outside_in in drupal_get_filename() (line 250 of core/includes/bootstrap.inc).

@lrix sorry this because the machine name of the module has changed in #2803375: Rename Outside-in module to "Settings Tray" for real
This happened because it is an experimental module and changes like this can happen(but are rare).

The machine name of the module changed from outside_in to settings_tray.

You can read how to solve this problem generally here: https://www.drupal.org/node/2487215#drupal8

So this should the right command

drush sql-query "DELETE FROM key_value WHERE collection='system.schema' AND name='outside_in';"

This is giving me a lot of headache when trying to update from 8.3.7 to 8.5.
None of the general problem solvers from the 2487215 work for me.

It seems to me that something wasn't handled correctly or the database update isn't made or it's not working.

My issue is with drush cim where this happens (also I can't access administration):

[error]  Drupal\Core\Config\ConfigImporterException: There were errors validating the config synchronization. in Drupal\Core\Config\ConfigImporter->validate() (line 728 of /var/www/html/web/core/lib/Drupal/Core/Config/ConfigImporter.php). 
 [error]  The import failed due to the following reasons:
Unable to install the <em class="placeholder">outside_in</em> module since it does not exist. 

EDIT:
manually deleting outside_in: 0 from config core.extension.yml resolved the issue

Did you uninstall the experimental module before upgrading Drupal?

Nope.

That is the reason. You should be fine now.

Got same problem. Anyone know how to remove this annoying message?

My update to 8.5 is worse than an error message. The site no longer loads. The "missing" outside_in module has created the following issues:
Symfony\Component\DependencyInjection\Exception\ServiceNotFoundException: "You have requested a non-existent service "cache_context.outside_in_is_applied"." at /home/ccatoday/public_html/d8/core/lib/Drupal/Component/DependencyInjection/Container.php line 151
[14-Mar-2018 02:44:43 UTC] Uncaught PHP Exception Twig_Error_Loader: "Template "core/modules/outside_in/templates/outside-in-page-wrapper.html.twig" is not defined (Drupal\Core\Template\Loader\ThemeRegistryLoader: Unable to find template "core/modules/outside_in/templates/outside-in-page-wrapper.html.twig" in the Drupal theme registry.)." at /home/ccatoday/public_html/d8/core/themes/classy/templates/layout/html.html.twig line 51

I've tried what was advised here to no avail. The site won't load, so no login, no update.php. Any suggestions?

So the solution was here. I rolled back to the previous install of Drupal - 8.3.5 - uninstalled the system tray module and re-installed 8.5. It worked. But pretty messy changing machine names in core elements, experimental or not, and blindsiding us in the following release. Bad Drupal.

Thanks.

I am sorry you feel blindsided. From https://www.drupal.org/project/drupal/releases/8.4.0-rc1:

“The experimental Settings Tray module's machine name has been changed from outside_in to settings_tray to match user-facing labels. If you have Settings Tray installed on your site, you must uninstall it before upgrading to 8.4.0-rc1 to avoid fatal errors. You can simply re-enable it afterward; since the Settings Tray module does not store any data or configuration, this should not affect your site.) Following this rename, Settings Tray is now considered beta stability.”

What other communications channels would make sense? I think going forward experimental modules must themselves be beta before appearing in a packaged release so this kind of thing can’t happen.

Just wanted to let folks know #4 worked great for me on the 8.5 release of Drupal.

I also used the instruction in #4 successfully - I was running Drupal 8.6.7 at the time.
Thanks !!

Error: User warning: The following module is missing from the file system:
drush sql-query "DELETE FROM key_value WHERE collection='system.schema' AND name='MODULE_NAME';"

Related documentation https://www.drupal.org/node/2487215

The solution #4 is working for me.
drush sql-query "DELETE FROM key_value WHERE collection='system.schema' AND name='MODULE_NAME';"

#4 worked for me.

Thanks @Rar9. #4 works for me too.

Sorry if I come back to this

I got this message today. I use Drupal 8.8.1

The following module is missing from the file system: field_collection bootstrap.inc:291

yes I removed the field_collection module because it was deprecated.

But know I don't know if this has consequences.
or how can I rebuild the database without getting into trouble.

Can you help?
drush sql-query "DELETE FROM key_value WHERE collection='system.schema' AND name='outside_in';"

how should I adapt this Drush command line for my error?

Thanks

Have you tried:

drush sql-query "DELETE FROM key_value WHERE collection='system.schema' AND name='field_collection';"

When removing a module you need to uninstall it from Drupal via 'admin/modules/uninstall' and then you are safe to remove the module files.

I have deinstalled the module, but still I got this error.

but your Drush command line helped. The error is gone.
Thanks