Glad Cory was able to help you (he is Superman around here!), I would also suggest a couple of other things, to keep your Mac running "mean and clean":
1. Are you making backups? There are two schools of thoughts about backups, and a number of the folks around here use either method. One, of course, is Time Machine. That is an excellent tool for scheduling such backups, but remember, it only does files/folders. The backup it makes is not bootable. The other way is to use a backup/cloning tool like Carbon Copy Cloner (CCC) or SuperDuper!. Either one of those makes an
exact, bootable copy of your "system". Recovery is easy from such backups, but unless you either "schedule" them to run automatically, or run them manually on a frequent basis, neither backup will contain the latest information. For myself, I use SuperDuper!, and make such a backup/clone of each of my Macs once a week, to two separate external drives. That is sufficient for my purposes, but may not be applicable to another individual.
2. Assuming you do not have a more robust disk maintenance/repair program like Disk Warrior or TechTool Pro, you should use Disk Utility to "check out" your internal drive (of course, you can use it to check out external drives too). The way you should do that is to boot to the hidden Recovery Partition on your Mac. To do that, hold down the Command and R keys when you start up your Mac. If will take some time to get to the main menu, but it will eventually appear. This link describes what software is on that partition:
https://support.apple.com/en-us/HT201314. What you need to do is launch Disk Utility from there and have it 1) Verify and Repair your disk at the
Volume (ie, top) level, and 2) Verify and Repair permissions, and Verify and Repair the disk, at the
partition level.
3. Download, install, and run the excellent, venerable program called
Onyx. You can get it from here:
http://www.macupdate.com/app/mac/11582/onyx
Note that link is for the version you need with Yosemite. That program has been around for quite some time, has had numerous, excellent reviews, and performs quite a few beneficial tasks. I depend on it as part of my weekly disk repair/maintenance/backup (cloning) processing. By the way, Onyx also can Repair Permissions, but it does it for just about all software. Disk Utility does it only for Apple software.
4. Finally, try and make the effort to clean up unneeded items (files, folders, etc.) as often as you can. One obvious candidate are EMails that are no longer needed. But, when you delete an EMail, depending on what EMail client you use, it doe snot go away. For myself, that is the case for Outlook. So, every week I'll rebuild Outlook's database (Microsoft provides instructions how to do that), and those deleted EMails go away permanently.