Firstly, using the Mac OS, we would call it 'repairing permissions'. There is a built-in application to do this called 'Disk Utility' which you can find here ...
Repairing permissions is in no way the same thing as defragmenting a drive. The repair permissions function in Disk Utility does exactly that. It resets the ownership and permissions of the OS X Systems files and those applications that have installed Reciept packages with a bill of materials (BOM) in /Library/Receipts.
Defragmentation, reordering of files so they are on contiguous disk sectors and/or removing all the gaps between files is a completely different process. There are some automatic features in OS X that do at least some of that, on the fly. There is one function called hot banding where the most often used files, almost always system files, are identified and automatically move the that part of the hard drive that offers the fastest access. There is another function where files in a certain size range are automatically placed on contiguous sectors. However, both of these built in functions tend to increase disk fragmentation.
There are three third party utilities
Drive Genius,
TechTool Pro and
iDefrag will perform actual file and/or disk defragmentation on OS X.
There is a school of thought, which I do not subscribe to, that defragmentation is no longer necessary with Mac OS X Extended (journaled) drives but
this thread by Micromat Tech 3 on MacFixit presents a cogent counter argument to that school of thought.
