Messed up files?

[NoGi]

I'm getting a file list for Gallery instead of the Gallery since the latest update. Not sure what's gone wrong but looking at my folder, there seems to be a bunch that don't belong or are in the wrong spot?

total 18952
-rw-r--r--  1 root   root        180 Mar 30 15:51 404error.php
-rw-r--r--  1 root   root      11598 May 30 17:11 Application.php
-rw-rw-r--  1 apache apache    11744 May 30 17:11 Credits.txt
drwxr-xr-x 14 apache apache     4096 Oct 30  2015 admin
drwxr-xr-x  2 apache apache     4096 Jan 14 07:35 api
drwxr-xr-x 21 apache apache     4096 May 30 17:11 applications
drwxr-xr-x 11 apache apache     4096 May 30 17:18 blog
drwxr-xr-x  5 apache apache     4096 Apr 13 04:40 cache
drwxr-xr-x  7 root   root       4096 May 30 17:18 calendar
drwxr-xr-x  2 apache apache     4096 Apr 29  2014 ccs_files
drwxr-xr-x  6 root   root       4096 May 30 18:50 chat
-rw-rw-r--  1 apache apache    10245 Nov 27  2014 check_requirements.php
drwxr-xr-x  9 root   root       4096 May 30 18:51 cms
-rw-rw-r--  1 apache apache        0 Mar 30 15:51 conf_global.dist.php
-rw-rw-r--  1 apache apache     1210 May 30 17:08 conf_global.php
drwxr-xr-x 11 root   root       4096 May 30 18:54 core
drwxr-xr-x  2 root   root       4096 May 30 18:58 data
drwxr-xr-x  3 apache apache    36864 Jun  1 19:11 datastore
-rw-rw-r--  1 apache apache    10572 Nov 27  2014 dav.php
-rw-rw-r--  1 apache apache     1278 Nov 27  2015 error.html
-rw-r--r--  1 root   root       1396 Mar 30 15:51 error.php
-rw-rw-r--  1 apache apache 19057988 Nov 27  2014 error_log
drwxr-xr-x  4 root   root       4096 May 30 18:58 extensions
-rw-rw-r--  1 apache apache     1150 May 20  2015 favicon.ico
drwxr-xr-x  9 root   root       4096 May 30 18:56 forums
drwxr-xr-x  8 root   root       4096 May 30 18:56 gallery
drwxr-xr-x  2 apache apache    16384 May 30 18:58 hooks
drwxr-xr-x  3 apache apache     4096 May 20  2015 images
-rw-rw-r--  1 apache apache      433 Mar 30 15:51 index.php
-rw-rw-r--  1 apache apache    21199 May 30 17:11 init.php
-rw-rw-r--  1 apache apache    12522 Nov 27  2014 initdata.php
drwxr-xr-x 12 apache apache     4096 May 30 18:58 interface
drwxr-xr-x 14 apache apache     4096 Apr 29  2014 ips_kernel
drwxr-xr-x  2 apache apache     4096 Apr 29  2014 lofiversion
-rw-rw-r--  1 apache apache     1428 Nov 27  2014 media_path.php
drwxr-xr-x 11 root   root       4096 Mar 30 15:40 mobiquo
drwxr-xr-x  4 root   root       4096 May 30 18:59 modules
drwxr-xr-x 10 root   root       4096 May 30 18:58 nexus
drwxr-xr-x 20 apache apache     4096 Apr 11 06:37 plugins
drwxr-xr-x 13 apache apache     4096 May  6  2014 public
-rw-rw-r--  1 apache apache     2367 Nov 27  2014 robotstxt.txt
drwxr-xr-x  5 root   root       4096 May 30 18:59 setup
-rw-rw-r--  1 apache apache      719 Mar 30 15:51 sitemap.php
-rw-rw-r--  1 apache apache     2278 May 27  2015 sitemap.xml
drwxr-xr-x 14 root   root       4096 May 30 18:59 sources
drwxr-xr-x 41 apache apache     4096 Mar 30 15:08 system
drwxr-xr-x  2 root   root       4096 May 30 18:59 tasks
drwxrwxrwx  7 apache apache     4096 May 24 22:44 themes
drwxr-xr-x  2 root   root       4096 May 30 18:59 upg_100044
drwxr-xr-x  2 root   root       4096 May 30 18:59 upg_101030
drwxr-xr-x  2 root   root       4096 May 30 18:59 upg_40000
-rw-r--r--  1 root   root       2017 May 30 17:11 upgrade.php
-rw-rw-r--  1 apache apache     1206 Mar 30 15:51 upgrading.html
drwxr-xr-x 73 apache apache     4096 Jun  1 19:11 uploads