Please describe the problem.

The assistant does not sync file permissions so if you set something as executable it won't be set the same on the other repositories.

What steps will reproduce the problem?

On the first host:

$ echo -e '#!/bin/sh\necho "Hello World!"' > testscript
$ chmod ugo+x testscript 
$ ./testscript 
Hello World!
$ ls -l
total 4
-rwxr-xr-x 1 pedrocr pedrocr 30 May 31 20:00 testscript

And on the second host:

$ ls -l
total 4
-rw-r--r-- 1 pedrocr pedrocr 30 May 31 20:00 testscript
$ ./testscript
bash: ./testscript: Permission denied

What version of git-annex are you using? On what operating system?

$ git annex version
git-annex version: 4.20130516.1
build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP
local repository version: 4
default repository version: 3
supported repository versions: 3 4
upgrade supported from repository versions: 0 1 2
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.2 LTS
Release:    12.04
Codename:   precise

confirmed (but may be out of scope) --Joey