How to clean install OSX without formatting drive?
There is no easy way to do this. You can't clean install and keep your files because those files live as part of the OS. The OS knows where they are, what they are, the permissions etc.  Clean installing would be removing all parts of the OS and installing a the new OS and the links to those files, where it would not know it needs those files or what they are.

Alternatively you can try:


Create a New Partition (Say of 200GB)
Install a clean copy of OS X there
Copy 100GB of your files to the new partition
Delete those exact files on the old partition
Shrink old partition and expand new partition
And repeat last 3 steps till you have all files


But the best solution would be:


Buy external HD
Copy all files to external
Reinstall OS X
Copy files back