You may have to use the Recovery to re-install the OS X, and that would be able
to restore a complete system to your computer with any/all parts yours is lacking.
{There is a way to remove Dock preference files and then have the computer re-
store or rebuild them on startup, that is not something I've had to do; so cannot
recommend the process. And I'd have to search Apple support for instructions.}
Dock reset to default (OS X Yosemite)
• How to reset the OS X Dock to factory defaults:
http://www.idownloadblog.com/2014/10/14/how-to-reset-the-os-x-dock-to-factory-de faults/
• Help - How to Guides for mac OS X + iOS Users:
http://www.xlr8yourmac.com/tips/MacBasics_Guides.html
Since the symptom of the problem may not directly relate to a cure, the Dock
issue may only point to the fact you were messing around in system folders.
Would know what else is no longer correct in those locations? Not me.
Not sure if a Time Machine backup from an interval prior to your involvement in
moving system owned parts around, could be used to restore the system again.
But if you have one, then you may not need re-install via Recovery; you may be
able to repair by use of OS X Utilities> Disk Utility> Disk First Aid, from booted
recovery partition, that would have been installed in the computer's hard drive.
• OS X Tips - Using the Recovery HD:
http://pondini.org/OSX/RecoveryHD.html
• OS X: About OS X Recovery - Apple Support
And if the hard drive in the Mac has no recovery partition, there are other steps to try.
• OS X: About Recovery Disk Assistant - Apple Support
Not sure why you were looking to change any system or non-user account preference
files... Did you make a second user account (admin level) as a test to see if the OS X
has a problem from your involvement, or if the symptom is only your main user account?
Sometimes you can start up in Safe mode, then once that's active (login and see it says
Safe mode) you could see if the system can self-repair; it will try on start up. To get out
of Safe mode, you simply restart the computer without any keyboard buttons held.
• Try safe mode if your Mac doesn't finish starting up - Apple Support
• If a flashing question mark appears when you start your Mac - Apple Support
• Mac Basics: Time Machine backs up your Mac - Apple Support
• Mac OS X: How to start up in single-user or verbose mode - Apple Support
Not sure of the path you may try to restore function to your Mac, but the Recovery mode
where you can use OS X Utilities to repair the drive or repair permissions may help. If not
then a re-install of the system, could. A Time Machine backup from a time before you
moved system parts around, may help.
In any event...
Good luck & happy computing!