A problem regarding repo tool and SmartGit is, that repo tool creates symlinks for some files from the .git dir to the .repo dir. After opening a repository using SmartGit the config symlink gets replaced with a regular file. This breaks the "repo sync" command, because repo verifies that the symlinks are still correct.

The following symlinks are created by repo tool:

anders05@ubuntu:~/Dev/build-puck$ ls -l sources/myrepo/.git/
lrwxrwxrwx 1 anders05 anders05    52 Sep 28 10:53 config -> ../../../.repo/projects/sources/myrepo.git/config
lrwxrwxrwx 1 anders05 anders05    56 Sep 28 10:53 description -> ../../../.repo/project-objects/myrepo.git/description
-rw-rw-r-- 1 anders05 anders05    41 Sep 28 10:53 HEAD
lrwxrwxrwx 1 anders05 anders05    50 Sep 28 10:53 hooks -> ../../../.repo/project-objects/myrepo.git/hooks
-rw-rw-r-- 1 anders05 anders05 28936 Sep 28 10:53 index
lrwxrwxrwx 1 anders05 anders05    49 Sep 28 10:53 info -> ../../../.repo/project-objects/myrepo.git/info
lrwxrwxrwx 1 anders05 anders05    50 Sep 28 10:53 logs -> ../../../.repo/projects/sources/myrepo.git/logs
lrwxrwxrwx 1 anders05 anders05    52 Sep 28 10:53 objects -> ../../../.repo/project-objects/myrepo.git/objects
lrwxrwxrwx 1 anders05 anders05    57 Sep 28 10:53 packed-refs -> ../../../.repo/projects/sources/myrepo.git/packed-refs
lrwxrwxrwx 1 anders05 anders05    50 Sep 28 10:53 refs -> ../../../.repo/projects/sources/myrepo.git/refs
lrwxrwxrwx 1 anders05 anders05    53 Sep 28 10:53 rr-cache -> ../../../.repo/project-objects/myrepo.git/rr-cache
lrwxrwxrwx 1 anders05 anders05    53 Sep 28 10:53 shallow -> ../../../.repo/projects/sources/myrepo.git/shallow
lrwxrwxrwx 1 anders05 anders05    48 Sep 28 10:53 svn -> ../../../.repo/project-objects/myrepo.git/svn

After opening the repository with SmartGit:

anders05@ubuntu:~/Dev/build-puck$ ls -l sources/myrepo/.git/                                                                                                                                                
-rw-rw-r-- 1 anders05 anders05   452 Sep 28 10:54 config
lrwxrwxrwx 1 anders05 anders05    55 Sep 28 10:53 description -> ../../../.repo/project-objects/myrepo.git/description
-rw-rw-r-- 1 anders05 anders05    41 Sep 28 10:53 HEAD
lrwxrwxrwx 1 anders05 anders05    49 Sep 28 10:53 hooks -> ../../../.repo/project-objects/myrepo.git/hooks
-rw-rw-r-- 1 anders05 anders05 28936 Sep 28 10:53 index
lrwxrwxrwx 1 anders05 anders05    48 Sep 28 10:53 info -> ../../../.repo/project-objects/myrepo.git/info
lrwxrwxrwx 1 anders05 anders05    49 Sep 28 10:53 logs -> ../../../.repo/projects/sources/myrepo.git/logs
lrwxrwxrwx 1 anders05 anders05    51 Sep 28 10:53 objects -> ../../../.repo/project-objects/myrepo.git/objects
lrwxrwxrwx 1 anders05 anders05    56 Sep 28 10:53 packed-refs -> ../../../.repo/projects/sources/myrepo.git/packed-refs
lrwxrwxrwx 1 anders05 anders05    49 Sep 28 10:53 refs -> ../../../.repo/projects/sources/myrepo.git/refs
lrwxrwxrwx 1 anders05 anders05    52 Sep 28 10:53 rr-cache -> ../../../.repo/project-objects/myrepo.git/rr-cache
lrwxrwxrwx 1 anders05 anders05    52 Sep 28 10:53 shallow -> ../../../.repo/projects/sources/myrepo.git/shallow
-rw-rw-r-- 1 anders05 anders05    25 Sep 28 10:54 smartgit.config
lrwxrwxrwx 1 anders05 anders05    47 Sep 28 10:53 svn -> ../../../.repo/project-objects/myrepo.git/svn

So a minimal fix for this should prevent SmartGit from replacing the config symlink with a regular file.