In previous versions of os x, you would find a file named com.apple.dockfixup.plist located in /Library/Preferences. In OS X Yosemite, that file was moved to:
/System/Library/CoreServices/Dock.app/Contents/Resources/com.apple.dockfixup.plist
Using your favorite plist editor, you can edit what will show up in the dock by removing items from the add-app and system-app keys.
Once done, you will need to edit another file located in:
/System/Library/CoreServices/Dock.app/Contents/en.lproj/default.plist
Using your favorite plist editor, you can edit what will show up in the dock by removing items from the persistent-apps keys.
After removing the unwanted items from both plist files, create a new user to test your work. You should no longer see any of the items that you removed in the dock.
Feel free to play around with some of the other keys in the plist files. You can add default folders to the dock as well.
POST UPDATE: 11-8-14
The following commands will net the same result as the above.
This will delete the dock apps:
/usr/libexec/PlistBuddy -c "delete:add-app" /System/Library/CoreServices/Dock.app/Contents/Resources/com.apple.dockfixup.plist
This will delete the dock folders:
/usr/libexec/PlistBuddy -c "delete:add-doc" /System/Library/CoreServices/Dock.app/Contents/Resources/com.apple.dockfixup.plist