With hidden files shown in the Finder, you can locate and remove these in Time Machine (click for larger view). Luckily, Time Machine will back up all files on the system (hidden or not), so if you have that you can restore the files however, you cannot do this directly at first, since Time Machine will not show hidden files. While these examples are a bit extreme, sometimes when people are configuring their systems "under the hood" they may corrupt a specific file or folder that they would like to restore. As a result, not only would you break the system but you would delete all of your data. The mistake here is to put a space between the tilde character and the rest of the command: this tells it to target all the files within the current user's home directory in addition to all the files in the system's "/etc" folder and remove them. The third command would have even greater consequences. This folder contains numerous configuration files for system services and removing it would essentially break much of the underlying structure of OS X. Without the tilde character (which specifies the path to the current user's home directory), the second command would remove the system's "/etc" folder that is at the root of the hard drive. The first command would target and remove a folder "etc" within the current user's home directory, but the second and third commands would have devastating effects on the system. For instance, take a look at these three commands (do not run them): This type of error is easy to make, especially if you are using the Terminal to remove files and inadvertently miss a simple character.
Recently in the Apple Support Communities forum user " uwes98" had difficulties after uninstalling the technical computing application Matlab and removing the hidden "/etc" file at the root of the filesystem instead of the one Matlab had created in his home directory. In reality there are a number of hidden files and folders that help govern the behavior of OS X, and occasionally when configuring software packages you have to interact with these items.
The only folders you see are the system folder, applications folder, user home directories, and a few others that might be useful when configuring the system for your needs. The filesystem in OS X is relatively clean by default when viewed through the Finder.
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