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Sorry to hear you are having issues. Have you been making backups of your entire system? SuperDuper! is an excellent tool for doing just that. With a bootable backup like the one SuperDuper! creates, you can boot from that backup, and do disk maintenance/repairs/software diagnosis, etc. in a more isolated environment.
Short of that, hopefully the (hidden) Recovery HD partition is on your internal drive. To see if it is there, launch Disk Utility, and the next to the last Menu Heading is Debug (right next to the last one, Help). Click on that, and near the bottom, one of the choices says "Show every partition ...". Click on that, and it will immediately show (on the list of devices/partitions to the left whether the Recovery HD partition is there. If it's not there, there are a couple of ways of getting it onto your hard drive, but you will need the Install OS X Yosemite file. It is typically in the Applications folder, but it goes away after an OS installation (not update). That's why it is always a good idea to have a copy of it in other locations. If you don't have it, you can download it from the Apple store.
Assuming you have it, you can boot into it by holding down the Command and R keys when you start up your machine. Eventually you'll get a screen that has (I believe) 4 menu choices. One of them says Disk Utility, I believe (I use TechTool Pro instead for disk maintenance/repairs, so I'm not quite sure what it says). In any event, when you select Disk Utility, you need to do the following:
1. At the "Volume" level, do a Verify and Repair Disk.
2. At the "partition" level, do a Verify and Repair Permissions, and also a Verify and Repair Disk. (I assume that will work just fine for the Windows-related partition, but you might want to make sure.
Note that when one repairs permissions using Disk Utility, it only repairs such permissions on Apple software. So, I would recommend you download the excellent freeware product Onyx. Besides repairing permissions for all software, it has some limited disk maintenance/repair functions, and quite a few cleanup ones. You can get Onyx from here:
http://www.macupdate.com/app/mac/11582/onyx
Since you are using Yosemite, that is the exact version you want.
Also, not sure if it will help or not, but a new version of Yosemite, OS 10.10.3, came out on Wednesday. If you have not upgraded yet to that version, I suggest using the Combo Updater. You can get it from here:
https://support.apple.com/kb/DL1804?locale=en_US
Short of that, hopefully the (hidden) Recovery HD partition is on your internal drive. To see if it is there, launch Disk Utility, and the next to the last Menu Heading is Debug (right next to the last one, Help). Click on that, and near the bottom, one of the choices says "Show every partition ...". Click on that, and it will immediately show (on the list of devices/partitions to the left whether the Recovery HD partition is there. If it's not there, there are a couple of ways of getting it onto your hard drive, but you will need the Install OS X Yosemite file. It is typically in the Applications folder, but it goes away after an OS installation (not update). That's why it is always a good idea to have a copy of it in other locations. If you don't have it, you can download it from the Apple store.
Assuming you have it, you can boot into it by holding down the Command and R keys when you start up your machine. Eventually you'll get a screen that has (I believe) 4 menu choices. One of them says Disk Utility, I believe (I use TechTool Pro instead for disk maintenance/repairs, so I'm not quite sure what it says). In any event, when you select Disk Utility, you need to do the following:
1. At the "Volume" level, do a Verify and Repair Disk.
2. At the "partition" level, do a Verify and Repair Permissions, and also a Verify and Repair Disk. (I assume that will work just fine for the Windows-related partition, but you might want to make sure.
Note that when one repairs permissions using Disk Utility, it only repairs such permissions on Apple software. So, I would recommend you download the excellent freeware product Onyx. Besides repairing permissions for all software, it has some limited disk maintenance/repair functions, and quite a few cleanup ones. You can get Onyx from here:
http://www.macupdate.com/app/mac/11582/onyx
Since you are using Yosemite, that is the exact version you want.
Also, not sure if it will help or not, but a new version of Yosemite, OS 10.10.3, came out on Wednesday. If you have not upgraded yet to that version, I suggest using the Combo Updater. You can get it from here:
https://support.apple.com/kb/DL1804?locale=en_US