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upgrade from 3.1 to 4.0.1 - git config in repos wrong or missing

Created by: technodrome

To upgrade, I used this guide: https://github.com/gitlabhq/gitlabhq/wiki/From-3.1-to-4.0

As I didn't find any info on direct upgrade from 3.1 to 5, I upgraded incrementally. First of all I upgraded Gitolite to v3 as per https://github.com/gitlabhq/gitlabhq/wiki/Reinstall-gitolite. No problems during this process. However, 4.0.1 app check fails:

(help messages omitted and everything other is green)

gitlab@xxx:~/gitlab$ bundle exec rake gitlab:check RAILS_ENV=production
.
.
gitlab user is in git group? ... no

gitlab user actually is in git group. It is: gitlab : git rvm

Git config in repos: ...
ProjectA ... wrong or missing
ProjectB ... wrong or missing
ProjectC ... wrong or missing
ProjectD ... wrong or missing
ProjectE ... ok

Init script up-to-date? ... no

Projects have satellites? ...
ProjectA... can't create, repository is empty
ProjectB ... yes
ProjectC ... can't create, repository is empty
ProjectD ... yes
ProjectE ... yes

I am unable to locate the source of the problem. However, this may be related: Section 3. Update post-receive hooks (Requires gitolite v3 ), Step 2. states: 2. Run script

sudo -u git -H lib/support/rewrite-hooks.sh

The result is:

root@xxx:/home/gitlab/gitlab# sudo -u git -H lib/support/rewrite-hooks.sh
ln: creating symbolic link `/home/git/repositories/smith/hooks/post-receive': No such file or directory
ln: creating symbolic link `/home/git/repositories/jenkins/hooks/post-receive': No such file or directory

Above mentioned directories contain the following data:

root@xxx:/home/git/repositories# ls -la

drwsrws---  7 git    git 4096 Feb 21 13:33 ProjectA.git
drwsrws---  7 git    git 4096 Feb 21 13:33 ProjectB.git
drwsrws---  8 git    git 4096 Feb 21 13:32 gitolite-admin.git
drwxrws---  2 gitlab git 4096 Feb 21 13:54 jenkins
drwsrws---  7 git    git 4096 Feb 21 13:33 ProjectC.git
drwxrws---  2 gitlab git 4096 Feb 21 13:54 smith
drwsrws---  7 git    git 4096 Feb 21 13:33 ProjectD.git
drwsrws---  7 git    git 4096 Feb 21 13:33 ProjectE.git
drwsrws---  7 git    git 4096 Feb 21 13:32 testing.git

smith and jenkins directories are empty.

My environment: OS Debian squeeze 6.0.6, Linux 2.6.32-5-686 Ruby /usr/local/rvm/rubies/ruby-1.9.2-p320/bin/ruby RVM 1.13.6 (stable) RubyGems 1.8.24

Please guys, any ideas?