Why is my Application's Icon grayed out in OS X Lion?

Question

In the Applications folder on OS X I have a few programs that are "grayed out":

I tried running Repair Disk Permissions in the Disk Utility but it doesn't fix this.

I tried looking at the permissions manually in Terminal:

$ ll /Applications | grep -E Goo\|Mate

drwxr-xr-x@   3 cwd  wheel        102B Sep 25 04:15 Google Chrome.app
drwxr-xr-x@   3 cwd  admin        102B Mar 14  2011 TextMate.app

This behavior is preventing the Apps from showing up in Spotlight Search and also Quicksilver.

I don't know much about extended attributes but I'm going to try and provide a little more info:

$ xattr TextMate.app/
com.apple.FinderInfo

And possibly this will also help:

$ xattr -l TextMate.app
com.apple.FinderInfo:
00000000  00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00  |........@.......|
00000010  00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  |................|
00000020

• Why is this happening?
• How can I fix it?

Update

Per @danielbeck's request, the results of

ls -lae@ /Applications/{TextMate,iTunes,Growl,Google\ Chrome}.app/Contents/MacOS

output:

drwxrwxr-x@ 3 root  wheel    102 Sep 25 05:09 .
    com.apple.FinderInfo       32 
drwxrwxr-x@ 8 cwd   wheel    272 Sep 25 05:09 ..
    com.apple.FinderInfo       32 
-rwxrwxr-x  1 root  wheel  14048 Sep 25 05:09 Google Chrome

Growl.app/Contents/MacOS:
total 744
drwxr-xr-x   3 root  wheel      102 Sep 19 18:51 .
drwxr-xr-x  12 root  wheel      408 Oct 14 23:19 ..
-rwxr-xr-x   1 root  wheel  1204176 Oct 14 23:19 Growl

TextMate.app/Contents/MacOS:
total 22856
drwxr-xr-x  3 cwd   admin       102 Mar 15  2011 .
drwxr-xr-x  7 cwd   admin       238 Mar 13  2011 ..
-rwxr-xr-x  1 cwd   admin  11700088 Mar 15  2011 TextMate

iTunes.app/Contents/MacOS:
total 98240
drwxr-xr-x   9 root  wheel       306 Oct  2 09:37 .
drwxr-xr-x  10 root  wheel       340 Oct  2 09:37 ..
-rwxr-xr-x   1 root  wheel  40631056 Sep 10 01:34 iTunes
-rwxr-xr-x   1 root  wheel     34448 Sep 10 01:34 iTunesASUHelper
drwxr-xr-x   3 root  wheel       102 Oct  2 09:37 iTunesHelper.app
-rwxr-xr-x   1 root  wheel   6591200 Sep 10 01:34 libgnsdk_dsp.1.9.5.dylib
-rwxr-xr-x   1 root  wheel    563040 Sep 10 01:34 libgnsdk_musicid.1.9.5.dylib
-rwxr-xr-x   1 root  wheel   1882736 Sep 10 01:34 libgnsdk_sdkmanager.1.9.5.dylib
-rwxr-xr-x   1 root  wheel    582536 Sep 10 01:34 libgnsdk_submit.1.9.5.dylib

As seen in the Finder:

Answer 1

This seems odd and I've not seen it, but side loaded apps should have permissions similar to the snapshot below. I would use finder to change the admin group to read only to ensure you can make changes to this folder and then revert the permissions to match mine below:

The posix and ACL permissions should be as follows for Chrome out of the box...

Air:~ mike$ls -lO /Applications/Google\ Chrome.app/
total 0
drwxrwxr-x  8 mike  admin  - 272 Oct 10 03:57 Contents
Air:~ mike$ls -lae@ /Applications/Google\ Chrome.app/
total 0
drwxrwxr-x   3 mike  admin   102 Oct 10 03:09 .
drwxrwxr-x+ 74 root  admin  2516 Oct 28 20:48 ..
 0: group:everyone deny delete
drwxrwxr-x   8 mike  admin   272 Oct 10 03:57 Contents

Unless you've gotten the launch services database in a muss or somehow enabled gatekeeper, it's likely a sign the app folders are not readable or executable by your OS user.

Answer 2

I encountered the same problem with Chrome in El Capitan (so quite a time after you asked). After OSX restart it always showed grayed-out, then on first run its icon turned full-color.

Per this advice I used:

defaults write com.apple.Dock showhidden -bool NO

and it stopped making the icon grayed-out on boot (likewise turning it YES again caused Chrome to appear grayed-out again, although on boot, not after killall Dock)