Howdy Justin, 

We don't have enough info to diagnose what's going on,  but DB corruption strikes me a more likely cause of your headaches than OS or Apache issues.

Based on your description, it sounds like Omeka thinks it is not properly installed -- i.e. mod_rewrite is probably fine. Before tearing your hair out messing with Apache, I'd recommend a performing a full DB recovery and verifying the connection since that will only take a few min. If that doesn't help, do a full Omeka restore (DB and files) presuming you don't just have an easy machine snapshot you can recover. Worst case scenario is to fall back on your bare metal recovery procedure.

Kyle

> On May 9, 2016, at 1:29 PM, Justin Snow <[log in to unmask]> wrote:
> 
> I have a few platforms (domain.com/omeka, domain.com/wordpress, domain.com/omeka-s) living alongside each other on an Azure cloud server running Ubuntu 14.04.4 and Apache 2.4. A few days ago, I tried installing an additional platform, but doing so seemed to break everything else on the server, so I removed it and reinstalled Apache. After editing the .htaccess file to remove a typo, everything worked. I left for the weekend, came back to work this morning, and everything is broken again.
> 
> By broken, I mean every URL on the server redirects to a mod_rewrite installation error page for Omeka (domain.com/install). Omeka has already been installed and running for months. MR needs to be enabled for Omeka to be installed and function properly. MR is definitely enabled.
> 
> 
> $ sudo a2enmod rewrite
> Module rewrite already enabled
> 
> 
> I'm assuming this is a problem with either the /var/www/.htaccess file or the /etc/apache2/apache2.conf file. Here's the relevant .htaccess code that is default for Omeka:
> 
> 
> RewriteEngine on
> 
> RewriteCond %{REQUEST_FILENAME} -f
> RewriteRule !\.php$ - [C]
> RewriteRule .* - [L]
> 
> RewriteRule ^install/.*$ install/install.php [L]
> RewriteRule ^admin/.*$ admin/index.php [L]
> RewriteRule .* index.php
> 
> 
> And here's the relevant(?) apache2.conf code:
> 
> 
> <Directory />
>    Options FollowSymLinks
>    AllowOverride All
>    Require all denied
> </Directory>
> 
> <Directory /usr/share>
>    AllowOverride None
>    Require all granted
> </Directory>
> 
> <Directory /var/www/>
>    Options Indexes FollowSymLinks MultiViews
>    AllowOverride All
>    Require all granted
> </Directory>
> 
> AccessFileName .htaccess
> 
> 
> If I remove the .htaccess file, or if I just remove some of RewriteRules, everything on the server is inaccessible (including Wordpress & Omeka-S). I'm clearly missing something. Any ideas?