Using Installer application can damage OS X; preventing startup, corrupting files

According to an article posted on stepwise.com, using Apple's Mac OS X Installer application (e.g., as found in the Utilities folder) can cause damage to your Mac OS X volume. Matt Fago had exactly this problem: "In my case, it erased the System directory once, and changed the permissions on the Applications directory the second time." Here is a quote from the article:

The Installer uses pax as the archiver instead of a tar derivative. Pax, in spite of its name meaning peace, doesn't necessarily play well with existing directories on your installation. This can cause serious problems.

First, if during the installation of a package pax encounters a directory that already exists, it will set its permissions and ownership to the permissions of the version in the archive. This is especially annoying in the case of the /Library or Applications directories, since many packages install into this location. However, it can have a much more serious impact, including preventing your system from booting, or applications from running.

The second, much more serious problem, is the interaction that pax will have with symbolic links that it encounters during installation. If you have a symbolic link that points to another directory, pax will replace the link with a directory and any files below that directory will be installed in place. This can also have serious side effects, including disabling your system completely.

A common situation is that a package will install a configuration file into /etc/somefile for some unix utility. However if the package hasn't been created using /private/etc/somefile as the destination, the link to /etc will be written over. This can easily have unexpected side effects (your system will not boot), and is one very common case where the package creator needs to be cautious.

We have not yet been able to personally test and confirm these claims, but they appear well documented.