iOS is so locked down that disabling protections in order to install your own modifications is called "jailbreaking." But OS X has remained free and easy--until now. El Capitan adds some security improvements that should make OS X more resistant to exploitation by malware, but it will also mean a change or end to some software utilities on which you may rely.
OS X includes System Integrity Protection, discussed in early June at Apple's annual Worldwide Developer's Conference, which will prevent the modification or removal of certain system files, among other changes. By locking more of the core system down, it adds another hurdle to any malware that needs to fiddle with things that typically don't need to be modified. Apple provides a way to disable this protection, but it's unlikely that most regular users will avail themselves of it.
(Side note: Before installing an El Capitan beta--either the public or developer version--you should check the blogs and newsletters of third-party developers on whose software you rely, particularly utilities that modify system behavior, like in dialog boxes or menus.)
The root of the problem
System Integrity Protection lets OS X operate normally while removing administrative overrides to modify a number of files, folders, running processes--software that manages tasks in the background--and system apps, like the Finder. It's been labeled rootless, because Unix has long been based around the notion that a superuser, called root, can do anything to the system she or he wants to.
Regular, non-root users have more limited access, which made sense for simultaneous multi-user systems, like servers, or workstations which different people use at various times--while sitting in front of them or remotely--and no one person should be able to muck things up for anyone else. The root user was both a god within the system and a bulwark against regular users.
OS X's Unix foundation gives the potential of root-level permission to any user who has administrator privileges, however, and you need those privileges to install many kinds of software. The first user created in the setup process for a new Mac has to have administrator privileges to create other accounts, modify security setups, and handle other tasks.
However, because one or more users can gain this kind of power, it renders OS X vulnerable to both local and remote attacks: A malicious local user could run software that escalates privileges, gaining root when they're not supposed to; a remote attacker might install malware through an exploit, which then gets root and takes over the machine. Some malware's entire vector of attack is as a Trojan horse: Convincing a user that it's legitimate, so that they type in their password to install it.
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