scruffy,
What fryke and I are trying to tell everyone is that there are reasons people should abide by Apple's rules regarding the locations of applications and utilities. Mac OS X ≠ Mac OS 9. These are two very different beasts. Mac OS X's UNIX underpinings use UNIX symbolic links which are similar to Aliases but are not the same. If some program depends on another and goes looking for it where it is supposed to be and can't find it, "problems" may happen, instability occurs, systems crash, data gets corrupted, and you're a REALLY unhappy camper. It makes sense to leave things as they were intended and to substitute Aliases pointing to the actual application locations rather than to rearrange the applications into some order that makes sense to you. Think of it this way, everything you see on your screen is a LIE! Yes, Apple is LYING to us all! You see a graphical representation of the files and directories in the computer. There aren't any windows in an operating system, it's a representation of a directory. There aren't any icons in a computer, they are a graphical representation only for the user to easily recognize a file at a glance. Extending this representation to organize aliases pointing to files and directories is no different, and in fact is safer than rearranging the files themselves. What happens if you accidentally delete the alias? You just create a replacement. Delete the file and your going to have to reinstall from CD or download from the internet.
Apple is basing their new operating system on UNIX and this is what has been done since the beginning in UNIX, it is a standard, and Apple is going to follow standards. As the Slashdot folks commonly joke about the Mac folk, we will have to grow brains or suffer.
Apple has preserved as much as possible the traditional Macintosh experience with Aqua, purposely separating Aliases from UNIX symbolic links. We don't need to know how UNIX works, we just need to be aware that it has requirements and just follow the rules.
To show you just how twisted Mac OS 9 can be (I'm sure others here will chuckle after reading this), my brother complained (calls me all the time about problems with his computer) to me that he lost all of his MP3's when he reinstalled Mac OS 9 on his iMac. I told him that was impossible because the installer only rewrites the System folder. His reply was "well I lost everything, all my Quicken data too". I went over to his house some time after ward to see why this happened. It turns out ALL his MP3's were being stored in the "Apple Menu Items" folder inside his System Folder. He wanted to single click a song from the Apple Menu in Mac OS 9 to launch MacAMP. In fact, all his data was strewn all over inside his System Folder: he had files and folder located in the Extensions folder, the Preferences folder. He saved data whatever a program's first pick for a folder was. I couldn't believe what I saw. I YELLED AT HIM! NO! NO! NO! And promptly set him straight: You just don't do these things!