@TiagoTiago

Try to understand following: As you can see from anthonie´s picture programs are not usually installed to ONE directory. They are scattered across different directories.

Moreover what do you gain from if you were able to install program to ONE directory. You could surf there with explorer or from cli and then what? What do you gain from all that? Now you have filesystem that puts config files to one directory (generally in your home directory) and executables to another. Actually IIRC home directory has been for ages place for different config files so if you backup ONLY your home directory you backup also all program settings. If system crashes just install everything back and pull home directory backup and you have specific programs back to configuration what you had before crash.

And as said you have total freedom because of symlinkin.

Optification is something that is specific to N900. No need to worry. Just use apps from extras. If you choose to install stuff from testing and devel, then as their description says, test and report and fix by yourself. And I bet that if we had option to choose where to install then quite many N900 would be pretty much breaking all over the world because of user errors.