Repository still empty after push

Summary

First of all, sorry if my English is bad, i'll try to do my best.

After i created a new repository, made my first commit and then push to the origin (on Gitlab), the repository still empty. I tried to "Trigger a repository check" but nothing happens...

After i run sudo -u git -H bundle exec rake cache:clear RAILS_ENV=production the repository show all the changes, but i need to do it for every time a new project is made...

I can clone the repository and see all the changes i made, but it doesn't appear in Gitlab.

You can see that Gitlab think that the repository "Joël Sunier / test" is empty (in the GitLab Application Check)

Steps to reproduce

Create a new repository and push the first commit to Gitlab. Then, go to Gitlab on the project and you should see an empty project.

Expected behavior

The commits i made, all branches, all files, etc...

Relevant logs and/or screenshots

githost.log:

Started GET "/api/v3/internal/check" for 127.0.0.1 at 2016-06-26 22:25:11 +0200
** [Raven] Raven 0.15.6 configured not to send errors.
Scoped order and limit are ignored, it's forced to be batch order and batch size
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:25:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:25:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:26:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:26:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:27:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:27:30 +0200
** [Raven] Raven 0.15.6 configured not to send errors.
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:28:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:28:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:29:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:29:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:30:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:30:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:31:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:31:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:32:30 +0200
Started GET "/jsunier/test.git/info/refs?service=git-upload-pack" for 80.219.12.191 at 2016-06-26 22:32:30 +0200

Before/After the push:

Project recently created

Proof that everything is up-to-date:

git push -u origin master

After clearing the cache:

After clearing the cache

Output of checks

Results of GitLab Application Check

Checking GitLab Shell ...

GitLab Shell version >= 2.7.2 ? ... OK (2.7.2)
Repo base directory exists? ... yes
Repo base directory is a symlink? ... no
Repo base owned by git:git? ... yes
Repo base access is drwxrws---? ... yes
hooks directories in repos are links: ...
Stogon / TheCommunity ... ok
Joël Sunier / SLSTV ... ok
Stogon / stogon.io ... ok
Joël Sunier / usinacraft.ch ... ok
Stogon / Qmark ... ok
Nutr4x / Qmark ... ok
Joël Sunier / Qmark ... ok
Linion / backup-marry ... ok
Nutr4x / stogon.io ... ok
Nutr4x / NodeJs ... ok
Nutr4x / Nutr4x-Web ... ok
Nutr4x / LolSqlite ... ok
Joël Sunier / lajrn.ch ... ok
Joël Sunier / karpas-sports.ch ... repository is empty
Joël Sunier / test ... repository is empty
Running /home/git/gitlab-shell/bin/check
Check GitLab API access: OK
Check directories and files:
        /home/git/repositories: OK
        /home/git/.ssh/authorized_keys: OK
Test redis-cli executable: redis-cli 3.0.3
Send ping to redis server: PONG
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

Running? ... yes
Number of Sidekiq processes ... 1

Checking Sidekiq ... Finished

Checking Reply by email ...

Reply by email is disabled in config/gitlab.yml

Checking Reply by email ... Finished

Checking LDAP ...

LDAP is disabled in config/gitlab.yml

Checking LDAP ... Finished

Checking GitLab ...

Git configured with autocrlf=input? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config outdated? ... no
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory setup correctly? ... yes
Init script exists? ... yes
Init script up-to-date? ... yes
projects have namespace: ...
Stogon / TheCommunity ... yes
Joël Sunier / SLSTV ... yes
Stogon / stogon.io ... yes
Joël Sunier / usinacraft.ch ... yes
Stogon / Qmark ... yes
Nutr4x / Qmark ... yes
Joël Sunier / Qmark ... yes
Linion / backup-marry ... yes
Nutr4x / stogon.io ... yes
Nutr4x / NodeJs ... yes
Nutr4x / Nutr4x-Web ... yes
Nutr4x / LolSqlite ... yes
Joël Sunier / lajrn.ch ... yes
Joël Sunier / karpas-sports.ch ... yes
Joël Sunier / test ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.1.0 ? ... yes (2.3.1)
Your git bin path is "/usr/local/bin/git"
Git version >= 2.7.3 ? ... yes (2.7.4)
Active users: 5

Checking GitLab ... Finished

Results of GitLab Environment Info

System information
System:         Ubuntu 15.10
Current User:   git
Using RVM:      no
Ruby Version:   2.3.1p112
Gem Version:    2.6.6
Bundler Version:1.12.5
Rake Version:   10.5.0
Sidekiq Version:4.1.2

GitLab information
Version:        8.8.4
Revision:       d4c3f17
Directory:      /home/git/gitlab
DB Adapter:     mysql2
URL:            http://git.stogon.io
HTTP Clone URL: http://git.stogon.io/some-group/some-project.git
SSH Clone URL:  git@git.stogon.io:some-group/some-project.git
Using LDAP:     no
Using Omniauth: yes
Omniauth Providers: github, twitter

GitLab Shell
Version:        2.7.2
Repositories:   /home/git/repositories/
Hooks:          /home/git/gitlab-shell/hooks/
Git:            /usr/local/bin/git

Possible fixes

The only fix i found for now is to clear the cache for every new project.