404 error after apache update

Steps to reproduce

  1. Apache update on my server
  2. Attempt to repair owncloud through occ command but occ file has disappeared from /var/www/owncloud folder and I get the message "Could not open input file: occ"
    3.

Expected behaviour

Reaching my owncloud online (mywebsite.com/owncloud), I would expect the login form.

Actual behaviour

404 error. Though reaching "mywebsite.com" only return the Apache2 default page, proving the server side is working properly.

Server configuration

Operating system: Ubuntu 16.04 LTS

Web server:

Database:

PHP version: 7.0

ownCloud version: (see ownCloud admin page) 10.0

Updated from an older ownCloud or fresh install: updated from owncloud 9

Where did you install ownCloud from:

Signing status (ownCloud 9.0 and above): not possible

Login as admin user into your ownCloud and access 
http://example.com/index.php/settings/integrity/failed 
paste the results into https://gist.github.com/ and puth the link here.

The content of config/config.php: config.php is empty

Log in to the web-UI with an administrator account and click on
'admin' -> 'Generate Config Report' -> 'Download ownCloud config report'
This report includes the config.php settings, the list of activated apps
and other details in a well sanitized form.

or 

If you have access to your command line run e.g.:
sudo -u www-data php occ config:list system
from within your ownCloud installation folder

*ATTENTION:* Do not post your config.php file in public as is. Please use one of the above
methods whenever possible. Both, the generated reports from the web-ui and from occ config:list
consistently remove sensitive data. You still may want to review the report before sending.
If done manually then it is critical for your own privacy to dilligently
remove *all* host names, passwords, usernames, salts and other credentials before posting.
You should assume that attackers find such information and will use them against your systems.

List of activated apps: not possible

If you have access to your command line run e.g.:
sudo -u www-data php occ app:list
from within your ownCloud installation folder.

Are you using external storage, if yes which one: local/smb/sftp/...

Are you using encryption: no

Are you using an external user-backend, if yes which one: LDAP/ActiveDirectory/Webdav/...

LDAP configuration (delete this part if not used)

With access to your command line run e.g.:
sudo -u www-data php occ ldap:show-config
from within your ownCloud installation folder

Without access to your command line download the data/owncloud.db to your local
computer or access your SQL server remotely and run the select query:
SELECT * FROM `oc_appconfig` WHERE `appid` = 'user_ldap';


Eventually replace sensitive data as the name/IP-address of your LDAP server or groups.

Just make a backup of the owncloud directory then download latest server package and decompress it and copy that over the old installation.
Then follow the manual upgrade guide using occ should work .

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