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 I've been syncronizing my data since long time, mainly using rsync or unison. Thus I had two 3.5Gb datasets set1 (usb drive, hfs+ partition) and set2 (hdd, ext4 ubuntu 13.04 box) which differed only in 50Mb (new on set1 ). This was double checked using diff -r before doing anything.
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 I created a git annex repo in direct mode for set2 from command line, and after that I let the assistant scan it.
 After that created the repo for set1 and added it to the assistant. I think here comes my mistake (I think).
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 Instead of keeping them apart, at told assistant to sync with set2.
 Why I think this was a mistake? Because set2 was indexed and set1 no, and I'm seeing a lot of file moving a copying, which in my humble opinion should not happen.
 What I expected it only the difference to be transferred from set1 to set2.
 What it seems to be doing is moving away all content in set1, and copying it back from set2. I think it will end correctly, but with a lot of unnecessary and risky operations.
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 I think I should have independently added both datasets, let them be scanned and then connect to each other.
 So, now the questions:
 1. Is that the correct way to proceed?