2012 Mac Mini becoming very slow when using finder

Question

Hi!
I've had my 2012 Mac Mini (10.9 Mavericks, Dual Booted W/ Windows) since February 2014 (Late to the party, I know) and, up until about a week ago, it was fine.
Then, all of a sudden, it starts being unusabley slow the moment I try to do anything in finder. Relaunching finder makes it a bit more bareable, and rebooting fixes it completely until I next open finder. I thought this may have been one of those rare times when a Mac gets a virus, however, AVG found nothing. The next thing I found was that it was to do with the fact that my hard drive was full (it was quite full) and that if I was using all of my 4GB of RAM that my Mac would use virtual memory, and that this would effect the speed if I didn't have a lot of HDD space. However, despite removing nearly 1/2 of the things on my HDD, the problem still persists. I have basically ruled out visiting "the local" apple store, as I'm in the middle of nowhere. the nearest one is around 3 hours away.
Thanks,
Dan

Answer 1

1. This is a comment on what you should—and should not—do to protect yourself from malicious software ("malware") that circulates on the Internet and gets onto a computer as an unintended consequence of the user's actions. It does not apply to software, such as keystroke loggers, that may be installed deliberately by an intruder who has hands-on access to the computer, or who has been able to log in to it remotely. That threat is in a different category, and there's no easy way to defend against it.
If you find this comment too long or too technical, read only sections 5, 6, and 10.
OS X now implements three layers of built-in protection specifically against malware, not counting runtime protections such as execute disable, sandboxing, system library randomization, and address space layout randomization that may also guard against other kinds of exploits.
2. All versions of OS X since 10.6.7 have been able to detect known Mac malware in downloaded files, and to block insecure web plugins. This feature is transparent to the user. Internally Apple calls it "XProtect."
The malware recognition database used by XProtect is automatically updated; however, you shouldn't rely on it, because the attackers are always at least a day ahead of the defenders.
The following caveats apply to XProtect:
It can be bypassed by some third-party networking software, such as BitTorrent clients and Java applets.
It only applies to software downloaded from the network. Software installed from a CD or other media is not checked.
As new versions of OS X are released, it's not clear whether Apple will indefinitely continue to maintain the XProtect database of older versions such as 10.6. The security of obsolete system versions may eventually be degraded. Security updates to the code of obsolete systems will stop being released at some point, and that may leave them open to other kinds of attack besides malware.
   3. Starting with OS X 10.7.5, there has been a second layer of built-in malware protection, designated "Gatekeeper" by Apple. By default, applications and Installer packages downloaded from the network will only run if they're digitally signed by a developer with a certificate issued by Apple. Software certified in this way hasn't necessarily been tested by Apple, but you can be reasonably sure that it hasn't been modified by anyone other than the developer. His identity is known to Apple, so he could be held legally responsible if he distributed malware. That may not mean much if the developer lives in a country with a weak legal system (see below.)
Gatekeeper doesn't depend on a database of known malware. It has, however, the same limitations as XProtect, and in addition the following:
It can easily be disabled or overridden by the user.
A malware attacker could get control of a code-signing certificate under false pretenses, or could simply ignore the consequences of distributing codesigned malware.
An App Store developer could find a way to bypass Apple's oversight, or the oversight could fail due to human error.
Apple has so far failed to revoke the codesigning certificates of some known abusers, thereby diluting the value of Gatekeeper and the Developer ID program. These failures don't involve App Store products, however.
   For the reasons given, App Store products, and—to a lesser extent—other applications recognized by Gatekeeper as signed, are safer than others, but they can't be considered absolutely safe. "Sandboxed" applications may prompt for access to private data, such as your contacts, or for access to the network. Think before granting that access. Sandbox security is based on user input. Never click through any request for authorization without thinking.
4. Starting with OS X 10.8.3, a third layer of protection has been added: a "Malware Removal Tool" (MRT). MRT runs automatically in the background when you update the OS. It checks for, and removes, malware that may have evaded the other protections via a Java exploit (see below.) MRT also runs when you install or update the Apple-supplied Java runtime (but not the Oracle runtime.) Like XProtect, MRT is effective against known threats, but not against unknown ones. It notifies you if it finds malware, but otherwise there's no user interface to MRT.
5. The built-in security features of OS X reduce the risk of malware attack, but they are not, and never will be, complete protection. Malware is a problem of human behavior, and a technological fix is not going to solve it. Trusting software to protect you will only make you more vulnerable.
The best defense is always going to be your own intelligence. With the possible exception of Java exploits, all known malware circulating on the Internet that affects a fully-updated installation of OS X 10.6 or later takes the form of so-called "Trojan horses," which can only have an effect if the victim is duped into running them. The threat therefore amounts to a battle of wits between you and the scam artists. If you're smarter than they think you are, you'll win. That means, in practice, that you always stay within a safe harbor of computing practices. How do you know when you're leaving the safe harbor? Below are some warning signs of danger.
Software from an untrustworthy source
Software of any kind is distributed via BitTorrent. or Usenet, or on a website that also distributes pirated music or movies.
Software with a corporate brand, such as Adobe Flash Player, doesn't come directly from the developer’s website. Do not trust an alert from any website to update Flash, your browser, or anything else.
Rogue websites such as Softonic and CNET Download distribute free applications that have been packaged in a superfluous "installer."
The software is advertised by means of spam or intrusive web ads. Any ad, on any site, that includes a direct link to a download should be ignored.
Software that is plainly illegal or does something illegal
High-priced commercial software such as Photoshop is "cracked" or "free."
An application helps you to infringe copyright, for instance by circumventing the copy protection on commercial software, or saving streamed media for reuse without permission.
Conditional or unsolicited offers from strangers
A telephone caller or a web page tells you that you have a “virus” and offers to help you remove it. (Some reputable websites did legitimately warn visitors who were infected with the "DNSChanger" malware. That exception to this rule no longer applies.)
A web site offers free content such as video or music, but to use it you must install a “codec,” “plug-in,” "player," "downloader," "extractor," or “certificate” that comes from that same site, or an unknown one.
You win a prize in a contest you never entered.
Someone on a message board such as this one is eager to help you, but only if you download an application of his choosing.
A "FREE WI-FI !!!" network advertises itself in a public place such as an airport, but is not provided by the management.
Anything online that you would expect to pay for is "free."
Unexpected events
You open what you think is a document and get an alert that it's "an application downloaded from the Internet." Click Cancel and delete the file. Even if you don't get the alert, you should still delete any file that isn't what you expected it to be.
An application does something you don't expect, such as asking for permission to access your contacts, your location, or the Internet for no obvious reason.
Software is attached to email that you didn't request, even if it comes (or seems to come) from someone you trust.
I don't say that leaving the safe harbor just once will necessarily result in disaster, but making a habit of it will weaken your defenses against malware attack. Any of the above scenarios should, at the very least, make you uncomfortable.
   6. Java on the Web (not to be confused with JavaScript, to which it's not related, despite the similarity of the names) is a weak point in the security of any system. Java is, among other things, a platform for running complex applications in a web page, on the client. That was always a bad idea, and Java's developers have proven themselves incapable of implementing it without also creating a portal for malware to enter. Past Java exploits are the closest thing there has ever been to a Windows-style virus affecting OS X. Merely loading a page with malicious Java content could be harmful.
Fortunately, client-side Java on the Web is obsolete and mostly extinct. Only a few outmoded sites still use it. Try to hasten the process of extinction by avoiding those sites, if you have a choice. Forget about playing games or other non-essential uses of Java.
Java is not included in OS X 10.7 and later. Discrete Java installers are distributed by Apple and by Oracle (the developer of Java.) Don't use either one unless you need it. Most people don't. If Java is installed, disable it—not JavaScript—in your browsers.
Regardless of version, experience has shown that Java on the Web can't be trusted. If you must use a Java applet for a task on a specific site, enable Java only for that site in Safari. Never enable Java for a public website that carries third-party advertising. Use it only on well-known, login-protected, secure websites without ads. In Safari 6 or later, you'll see a lock icon in the address bar with the abbreviation "https" when visiting a secure site.
Stay within the safe harbor, and you’ll be as safe from malware as you can practically be. The rest of this comment concerns what you should not do to protect yourself.
7. Never install any commercial "anti-virus" (AV) or "Internet security" products for the Mac, as they are all worse than useless. If you need to be able to detect Windows malware in your files, use one of the free security apps in the Mac App Store—nothing else.
Why shouldn't you use commercial AV products?
To recognize malware, the software depends on a database of known threats, which is always at least a day out of date. This technique is a proven failure, as a major AV software vendor has admitted. Most attacks are "zero-day"—that is, previously unknown. Recognition-based AV does not defend against such attacks, and the enterprise IT industry is coming to the realization that traditional AV software is worthless.
Its design is predicated on the nonexistent threat that malware may be injected at any time, anywhere in the file system. Malware is downloaded from the network; it doesn't materialize from nowhere.
In order to meet that nonexistent threat, commercial AV software modifies or duplicates low-level functions of the operating system, which is a waste of resources and a common cause of instability, bugs, and poor performance.
By modifying the operating system, the software itself may create weaknesses that could be exploited by malware attackers.
Most importantly, a false sense of security is dangerous.
8. An AV product from the App Store, such as "ClamXav," has the same drawback as the commercial suites of being always out of date, but it does not inject low-level code into the operating system. That doesn't mean it's entirely harmless. It may report email messages that have "phishing" links in the body, or Windows malware in attachments, as infected files, and offer to delete or move them. Doing so will corrupt the Mail database. The messages should be deleted from within the Mail application.
An AV app is not needed, and cannot be relied upon, for protection against OS X malware. It's useful, if at all, only for detecting Windows malware, and even for that use it's not really effective, because new Windows malware is emerging much faster than OS X malware.
Windows malware can't harm you directly (unless, of course, you use Windows.) Just don't pass it on to anyone else. A malicious attachment in email is usually easy to recognize by the name alone. An actual example:
London Terror Moovie.avi [124 spaces] Checked By Norton Antivirus.exe
You don't need software to tell you that's a Windows trojan. Software may be able to tell you which trojan it is, but who cares? In practice, there's no reason to use recognition software unless an institutional policy requires it. Windows malware is so widespread that you should assume it's in every email attachment until proven otherwise. Nevertheless, ClamXav or a similar product from the App Store may serve a purpose if it satisfies an ill-informed network administrator who says you must run some kind of AV application. It's free and it won't handicap the system.
The ClamXav developer won't try to "upsell" you to a paid version of the product. Other developers may do that. Don't be upsold. For one thing, you should not pay to protect Windows users from the consequences of their choice of computing platform. For another, a paid upgrade from a free app will probably have all the disadvantages mentioned in section 7.
9. It seems to be a common belief that the built-in Application Firewall acts as a barrier to infection, or prevents malware from functioning. It does neither. It blocks inbound connections to certain network services you're running, such as file sharing. It's disabled by default and you should leave it that way if you're behind a router on a private home or office network. Activate it only when you're on an untrusted network, for instance a public Wi-Fi hotspot, where you don't want to provide services. Disable any services you don't use in the Sharing preference pane. All are disabled by default.
10. As a Mac user you don't have to live in fear that your computer may be infected every time you install software, read email, or visit a web page. But neither should you assume that you will always be safe from exploitation, no matter what you do. The greatest harm done by security software is precisely its selling point: it makes people feel safe. They may then feel safe enough to take risks from which the software doesn't protect them. Nothing can lessen the need for safe computing practices.