How to handle the change to "Salesforce DX project format" and keep the revision history?

If the changes are not to complicated Git is able to recognized files moves without explicitly calling git mv as described here https://stackoverflow.com/questions/433111/how-to-make-git-mark-a-deleted-and-a-new-file-as-a-file-move.

I tested this myself using our internally used packaged travel expense app. A few month ago I was taking part in the DX Pilot and used

sfdx force:mdapi:convert --rootdir <retrieve dir name>

to convert the structure. Here is the commit which shows that all moves where recognized. I later reverted the structure back and the history of files is still there, across all the changes.