Please describe the problem.

with previous snapshot (6.20160119+gitgb2a2f5d-1~ndall+1) you just get a clean output

hopa:~/.tmp
$> git clone /home/yoh/.tmp/datalad_temp_clone_url_RmXPyt 123
Cloning into '123'...                    
done.

$> cd 123 
INFO.txt  test-annex.dat@  test.dat

$> git annex lookupkey test-annex.dat                                        
SHA256E-s4--181210f8f9c779c26da1d9b2075bde0127302ee0e3fca38c9a83f5b1dd8e5d3b.dat

with new one (6.20160126+gitg65f4442-1~ndall+1) you get it polluted in such a freshly cloned repo with

$> git annex lookupkey test-annex.dat                        
(merging origin/git-annex into git-annex...)
(recording state in git...)
SHA256E-s4--181210f8f9c779c26da1d9b2075bde0127302ee0e3fca38c9a83f5b1dd8e5d3b.dat

and since I am a "dude" who likes "devnulling" things for some reason (I hope reason is clear here ;)):

$> git annex lookupkey test-annex.dat 2>/dev/null            
(merging origin/git-annex into git-annex...)     
(recording state in git...)
SHA256E-s4--181210f8f9c779c26da1d9b2075bde0127302ee0e3fca38c9a83f5b1dd8e5d3b.dat

I guess I will just skip all lines starting with ( for now but thought to let you know about such changed behavior which might complicate pipelining etc

fixed --Joey