Issues after browser update

Ok so this is a weird issue I'm having, as we all know owncloud upgrades are usually problem-some. I have been updating either via console sometimes via web since OC7 and usually managed to figure those out myself. This time I did an upgrade from OC9.0.1.3 > 9.0.4 [stable] via web which went smooth after I took care of some file ownership issues I did a server restart and everything seemed fine until I went over to mydomain.com/server-status to check to apache status and noticed that it displayed the owncloud login page, I checked all system logs, apache logs and owncloud.log and nothing showed up. After fooling around with the php.ini settings with no luck I decided to rename the oc folder and install a fresh version of OC, same issue. Since the server is low usage I decided to reinstall my snapshot with digital ocean from a week prior, so that brings me back to OC9.0.1.3 and obviously there are no issues. I make sure that no system updates could of accounted for the problem by ONLY updating OC via the browser and same issue, shows me login page for oc. At this point I figure it's strictly an OC issue so I revert back to the snapshot of the update (9.0.4) and decide to rename the oc folder again and this time tested it by wget'ing wordpress and extracting the contents into the root directory and checked my /server-status. Boom it works, I remove the folder and replace it with my owncloud installation again, check it and same issue. Pretty much at this point in time I have done a days worth of diagnostics and testing only to conclude that the updater is bugged in my installation. Just as an FYI this happens to my info.php file as well and some other files I tested, HTML shows up fine though. Has anyone faced an issue like this and how did you resolve it, if not do you have any ideas? Thanks

Steps to reproduce
Read Above

Expected behaviour
Every page I visit (subdomain, subfolder etc) shows owncloud login page. It should show the contents of that page/directory.

Actual behaviour
/server-status & info.php and pretty much any other non html file shows the owncloud login page even though I'm in the actual directory, as if it was a parked domain or something.

Server configuration
Operating system: Ubuntu Linux 14.04.3
Web server: Server version: Apache/2.4.7 (Ubuntu) Server built: Jul 15 2016 15:34:04
Database: MySQL 5.5.50-0ubuntu0.14.04.1
PHP version: PHP 5.5.9-1ubuntu4.19
ownCloud version: 9.0.4
Updated from an older ownCloud or fresh install: Updated from 9.0.1.3

Special configuration (external storage, external authentication, reverse proxy, server-side-encryption): All traffic VIA 443, no domain name for install, encryption plugin used.

Integrity status for oC9+
No errors have been found.
(I did have a hash mismatch but extracted the two files from the archive and that fixed the hash issue)

Here is the log for the gui update
    Initializing
Current version is 9.0.1.3
Online version is 9.0.4 [stable]

Checking system
eChecking system health.e
- file permissions are ok.
Creating a checkpoint
Created checkpoint 9.0.1.3-57a2863376464
Downloading
Current version is 9.0.1.3
Online version is 9.0.4 [stable]
Downloaded 0% (0 of 39771461) Downloaded 100% (39771461 of 39771461)
Updating core
Extracting source into /var/www/html/cloud/_oc_upgrade/9.0.4
ownCloud or one of the apps require upgrade - only a limited number of commands are available
You may use your browser or the occ upgrade command to do the upgrade
Set log level to debug
Turned on maintenance mode
Checking whether the database schema can be updated (this can take a long time depending on the database size)
Checked database schema update
Checking updates of apps
Checked database schema update for apps
Updating database schema
Updated database
Starting code integrity check...
Finished code integrity check
Update successful
Turned off maintenance mode
Reset log level

Updating apps
Upgrading the application activity
Upgrading the application comments
Upgrading the application dav
Upgrading the application encryption
Upgrading the application federatedfilesharing
Upgrading the application federation
Upgrading the application files
Upgrading the application files_pdfviewer
ownCloud or one of the apps require upgrade - only a limited number of commands are available
You may use your browser or the occ upgrade command to do the upgrade
Set log level to debug
Turned on maintenance mode
Checking whether the database schema can be updated (this can take a long time depending on the database size)
Checked database schema update
Checking updates of apps
Checked database schema update for apps
Updating database schema
Updated database
Updating <files_pdfviewer> ...
Updated <files_pdfviewer> to 0.8.1
Starting code integrity check...
Finished code integrity check
Update successful
Turned off maintenance mode
Reset log level

Upgrading the application files_sharing
Upgrading the application files_texteditor
Upgrading the application files_trashbin
Upgrading the application files_versions
Upgrading the application files_videoplayer
Upgrading the application firstrunwizard
Upgrading the application gallery
Upgrading the application notifications
Upgrading the application provisioning_api
Upgrading the application systemtags
Upgrading the application templateeditor
Upgrading the application updatenotification
Upgrading the application external
Upgrading the application files_external
Upgrading the application user_external
Upgrading the application user_ldap
Finishing the update
Done
Done
All done!
This app will only backup core files (no personal data).
Please always do a separate backup of database and personal data before updating.
Backup     Done on          
9.0.1.3-57a28566bc09d     August 03 2016 19:59

I don't see any issue here. You probably just need disable index.php-less URLs of oC.

Remove:

'htaccess.RewriteBase' => '/',

from your config and run:

occ maintenance:update:htaccess

should do the trick.

Well that did fix the problem, BUT now I am getting Access Forbidden for OC with the error

Cannot serve directory /var/www/html/cloud/apps/files/: No matching DirectoryIndex (index.php,index.html) found, and server-generated directory index forbidden by Options directive.

Ofcourse I dont allow dir index for obvious reasons. For now I'll have to replace the two lines so I can access oc. EDIT: Does OC generate an .htaccess file on every install/update or is it a static file that changes based on versions.

Two Lines I Commented out:
RewriteRule . index.php [PT,E=PATH_INFO:$1]
RewriteBase /

BUMP
Bring Up My Posts Please.

You already solved your issue by removing that lines? What else do you need?

Sorry, I don't know if a mod marked it as solved or if I accidentally did. I said in the post that I replied to you that I get a cannot serve directory error when I remove those two lines which renders my install totally unusable.

Looks like something is really broken in your webserver. Maybe try a clean setup on Ubuntu 16.04 and use the official repositories. These are installing all needed dependencies and don't show these issues.

You could also do such an setup within a VM or use the 14.04 Community-Appliance from https://owncloud.org/install/#instructions-server and compare it with your setup to see where the difference is coming from

Well I use DigitalOceans repos which are directly from ubuntu anyways, before updating OC I ran server updates and oc updates without any problems. I think Ubuntu 16 comes with PHP7 now, how is compatibility with that. Also I just saw your update, I setup my vps from scratch including downloading the .tar from owncloud. I would hate to waste time and setup a whole new system and transfer over data, could the updater be bugged? Does the .htaccess change version to version.

Well dont look like anyone wants to help so ill close thread.

Its not about "no one wants to help". You got help here and information what to check why your environment behaves like this where other default environments don't show this issue.

You can't expect that anyone in here knows your webserver configuration or your environment. So only generic hints like above can be given.

I'm also marking this as unresolved again.