I do not believe the vagrant setup configures gitolite, you can just git clone using regular access:

git clone ssh://vagrant@pagure-dev.example.com:/path/to/git/repos

or

git clone /path/to/git/repos

if you mount some volumes into the vm

that doesn't work either atm, but this looks like a bug to me:
[vagrant@pagure-dev testing]$ grep url .git/config
url = /home/vagrant/repositories/testing.git/

[vagrant@pagure-dev testing]$ git push
Counting objects: 684, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (633/633), done.
Writing objects: 100% (684/684), 9.33 MiB | 7.80 MiB/s, done.
Total 684 (delta 84), reused 0 (delta 0)
remote: Resolving deltas: 100% (84/84), done.
remote: Empty compile time value given to use lib at hooks/update line 6.
remote: WARNING: Use of uninitialized value $repo in concatenation (.) or string at /usr/share/perl5/vendor_perl/Gitolite/Conf/Load.pm line 251, <DATA> line 1.
remote:
remote: FATAL: invalid repo ''
remote: error: hook declined to update refs/heads/master

remote: Empty compile time value given to use lib at hooks/update line 6.
remote: WARNING: Use of uninitialized value $repo in concatenation (.) or string at /usr/share/perl5/vendor_perl/Gitolite/Conf/Load.pm line 251, <DATA> line 1.
remote:

This is something in gitolite itself :(

The issue was reported 4 years ago, lot of things changed since then, also it was probably caused by gitolite itself based on the comments and logs, going to close this issue, don't see a doing from a pagure side.