Dear all,
     In the first place I will explain what I want to achieve and then the way I figured out to do it. I have a lot of scientific simulations which I need to be traceable (cross check experiment version with code version, etc). I run them mostly on my ubuntu box (14.10, ext4)  and store them on an indirect repo. From time to time, I find useful to work on them on my laptop (OSX 10.10, low disk space, hfs+). 
My idea was to full sync the main repo with a usb drive, and then at home get only the files I need to work from the USB drive.
I faced a huge interoperability problem regarding the filesystem format. I tried using ext4, hfs+, fat32 and exfat. Regarding performance and stability, exfat is the only usable option between linux and osx (using hfs+ got the repo corrupted many times while writing from linux). However that forces me to use either a direct mode repo on the USB drive or a bare one. 

Scenario 1: Direct mode on USB drive 
While this worked in another case, in this case when setting up the repo with the assistant it deleted all symlinks from the main repo. I wasn't able to correctly do this and finally gave up. 
Can anyone help me setting up this scenario? It will be like the following: 

* ubuntu box (ext4): main repo, indirect mode, all files
* usb drive (exfat): sync repo, direct mode, all files (having the files available is a plus)
* osx laptop (hpfs+): partial repo, indirect mode, some files


Scenario 2: Bare repo on USB drive 
In this case the bare repo gets synced, with all data (2.6Gb). However when I clone it on the laptop, I get the  message that files are not available, it says that they are only on main repo. This puzzles me because files seem to be on the bare repo.
What's wrong in this case? How can I debug this?
