HELP! Ghost files and empty Applications directory

Question

Just to set the stage of the issue, here's a what little background I have....
Im a long-time MacOSX user, and requested a Mac when starting my new job.  I started today and was given a hand-me-down Aluminum 27" iMac, running 10.6.8.  After some minor cleanup of someones old documents I started working, soon I stumbled into the "Home" directory and found the directory like this screen cap...
http://i951.photobucket.com/albums/ad355/KeyMedia/fileissues.jpg
Greyed out, ghosted files!?  From my first impression, it look like something I could just hopefully trash and move along, but it wasn't.  The "Move to Trash" progress bar/dialog box, got stuck.  I then went into "Force Quit" and re-launched the Finder.  After seeing that the files didn't make it to the trash, I tried it again with the same results.  THEN, I started digging around the home folder directories, and discovered that only 2 of the many applications that were already installed, populated in the "Applications" folder within the home directory!?  I had previously launched several apps before hand from the "stacks" folder that was already in the dock, as well as selecting the Applications shortcut in the sidebar of the finder, which populated all the apps!?  Seemed very strange and something I have never run across.  And just FYI, there is only one user account on the iMac.
A couple more qwirky things that happened through the course of the workday, was when trying to save to the "Desktop", made those files (.PDF & .RTF) invisible.  When I say invisible, I could not find those files anywhere on my system visually, but when going back into text-edit and doing a "Save-As" back to the desktop, the were visible on the Desktop, but only in the Save Dialog Box?!  After that finding I rebooted my Mac and after reboot, The files automatically appreared on the desktop, and didn't have that problem anymore today.
One more little thing....After the final reboot, a "ds.store" file appeared on my desktop?!  I haven't trashed that file, which it probably will not let me.  If im halfway correct, the "ds.store" files are normally placed within folders and directories to keep the MacOS file structure in place, and possiblly if deleted that it will get regenerated upon reboot, but again never tried to move this particular file fromt he desktop.
Looks to me like some preferences, or ds.store files got out of place and the file structure for the OS is out of place and isn't staying clean, but that is a big guess.
If anyone has any insight into these issues, what me be causing it, or what can fix it...I would greatly appreciate it!!
Thanks in Advance my fellow mac users!!

Answer 1

1. Open the Script Editor or AppleScript Editor in one of the subfolders of Applications and run the following:
tell application "Finder" to quit
if (do shell script "defaults read com.apple.finder AppleShowAllFiles") is "1" then
do shell script "defaults write com.apple.finder AppleShowAllFiles 0"
else
do shell script "defaults write com.apple.finder AppleShowAllFiles 1"
end if
delay 2
tell application "Finder" to run
2. Most of your applications are in the Applications folder at the top level of the drive, not the one in the home folder.
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