Missing applications after using Migration Assistant

Migration Assistant will move Apple and non-Apple information into a new computer. However, it may not move files that are in non-standard locations or files that it does not recognize.

It gets even tricker when the drive the data is coming from is having issues in the first place. Not an ideal situation in which to move data.

If you want an identical copy of a drive (mirror) you can use the Disk Utility program: http://support.apple.com/kb/HT1553. There are other programs out there that will clone your drive, but I've always found Disk Utility to be more than adequate for the job.

If you have a Time Machine backup of your computer you can do a full restoration, http://docs.info.apple.com/article.html?path=Mac/10.5/en/15638.html.
__NOTE: Because this is a full restore and not a migration, the drive will be erased and whatever was in your backup will be put on the drive in it's place.

This may not resolve the issue but it is a more complete restore than the migration so it might put back the files you are looking for.

Hope that helps.

MA will not restore files installed in the Unix directories unless you perform a full system restore.

Reinstalling all your Unix stuff is what you can do.

As MadisonP mentioned, if the original drive was failing then there is no guarantee that all of its files can be recovered. Since a drive can fail at any time, it is imperative that you maintain independent backups of anything on it that you cannot afford to lose. If this includes system level modifications or additions, your best bet is to clone the drive periodically, giving you a functional backup you can use immediately to continue working after drive problems occur.

You can do this with Disk Utility; however, the two most popular cloning utilities (Carbon Copy Cloner & SuperDuper!) provide features like automatic scheduling & "smart" backups that may better suit your needs. In particular, SuperDuper! includes a novel developer mode that lets you test different system configurations with one set of user folders that you may find useful.

It is the responsibility of every user to implement a backup strategy adequate for their situation. This is something nobody should neglect doing but of critical importance for developers & others depending on their computers for their livelihood.