Modules won't show up in the "Installed Mods" list, themes don't appear in "Appearances"

Why are you futzing with a release candidate rather than the 7.x-1.0 release of ACL? How are you even able to get to the rc1 version if you use the updater?

If this is so very urgent, why don't you just download and extract the ACL distribution archive to where you need it?

ACL is just the data here. No ACL code has run yet. I see no indication for a bug in ACL. Maybe someone in the core queue can help you...

I'm having a similar issue today.
I updated 3 different drupal installations, and two fo them are fine.
The third, I only updated 1 module (meta-tags),
and this happened. All my modules and themes were suddenly lost.
They are all still in sites/all/{modules,themes}, but no longer appearing in the admin interface, period.
I tried to install some of them (had to manually remove the existing files), and the uploader uploads them and tells me that they've been installed "successfully", but they do not appear in appearanced or modules interface to be enabled.
They are being uploaded with incorrect permissions (d------r-x). When I do chmod -R 755 to give them the proper permissions (drwxr-xr-x as is the case on my other, still functional sites), still no joy.
The themes/modules to not appear in the system table in the DB.
I then applied the update from 7.21 to 7.22 for drupal core, hoping maybe this would help.
Still, no joy.
All of the modules and themes are still "physically" in their proper location in sites/all/, but the admin interface shows none of them. If I manually remove them and re-install through the interface, they upload, but, still, do not appear in the admin interface. None of them are showing in the DB.
I found THIS particular thread, because the only error I find is similar:
Warning: fileperms(): stat failed for /var/www/newhaven/sites/all/modules/addtoany in Updater->makeWorldReadable() (line 356 of /var/www/newhaven/includes/updater.inc).

Same line of includes/updater.inc

The question I have at this juncture is (regardless of how they were lost, but so I can reinstall them now), why are they uploaded with improper permissions, and why are they not included in the DB in the system table when "installed" now.
I assume the answer to these two questions would allow me to resolve the issue.
Line 356 of includes/update.inc is
$new_perms = substr(sprintf('%o', fileperms($path)), -4, -1) . "5";
part of this function:
public function makeWorldReadable(&$filetransfer, $path, $recursive = TRUE) {
if (!is_executable($path)) {
// Set it to read + execute.
$new_perms = substr(sprintf('%o', fileperms($path)), -4, -1) . "5";
$filetransfer->chmod($path, intval($new_perms, 8), $recursive);
}
}

What themes are you running? Are you using an admin theme? try switching to Seven as the admin and see if that helps:)

You can also see

We need steps to reproduce from a clean Drupal installation if this is to be marked as a bug against core.

Changing to the Seven theme hasn't made any difference.

The theme I had installed before updating the meta-tag module was the Elegant theme by www.devsaran.com
I'm inclined to believe that the problem is with registering installed mods/themes in the database, and that something occuring while updating the meta-tag module caused the problem, although I updated the same module on other installations yesterday without issue.
On this particular installation, it hung for a long time in the update, unlike the others.
I'm considering reinstalling fresh, myself.
The site is small, only a few pages.
I could copy the content manually, dump the db, reinstall, and have the site back up within a couple of hours, probably.
Still, it would be interesting to know what's caused the problem.
There is one other thread, as indicated, with a similar error, mentioning the same particular line and file.
That thread shows no resolution.

If it's relevant, here is also a list of modules I had installed:
addtoany
ctools
i18n
l10n_update
metatag
token
translation_management
variable

Ok:)

How are your file permissions? This can be a major issue on 12.04lts as often noted. Can you try chown && chmod sites/all/modules just for now try chown -R username:username drupal/ && chmod -R 777 drupal/ to see if there is an access permissions issue. Often on our Ubuntu dev 12.04lts sites we run /var/www/drupal chown username:username && chmod 777 - There is a bit of an issue with ftp setup on drupal and ubuntu 12.04lts and 10.04lts really we have worked out of all of this just by using sudo drush pm-update and then setting chown and chmod wide open for speed.

Just for a question? Why is your apache2 set up on:
my drupal setup is located in /usr/share/drupal7/
my sites are located in /etc/drupal7/sites

Given the issues at hand it would seem to make sense to set you apache2 working directory @ /var/www/drupal

In addition I would look at your multi-site setup in /sites/mysite.com and the like. I would almost say this is a config issue for sure.

Hope that helps...

changed the listed host address