Issue Summary

This is reproducible on Data Center: (no)
App users permissions aren't properly set for projects created with Jira Custom templates.

Steps to Reproduce

1. Prepare a Jira Cloud Entreprise test site
2. Install a Connect app with READ WRITE and ADMIN scopes
3. Create a new team-managed business project with access set to private (this will be the source project)
4. Verify that the Connect app user has the BROWSE_PROJECTS, CREATE_ISSUES, ASSIGN_ISSUES and MANAGE_WATCHERS permissions in the source project
5. Save the new project as a project template, and use the template to create a new project (this will be the target project)
6. Verify that the new project is also private
7. Verify that the Deep Clone app user has the BROWSE_PROJECTS, CREATE_ISSUES, ASSIGN_ISSUES and MANAGE_WATCHERS permissions in the target project

Example API call

POST /rest/api/2/permissions/check
{
  "accountId": "appUserAccountId",
  "projectPermissions": [
    {
      "permissions": [
        "BROWSE_PROJECTS", "CREATE_ISSUES", "ASSIGN_ISSUES", "MANAGE_WATCHERS"
      ],
      "projects": [
        "projectId1", "projectId2"
      ]
    }
  ]
}

Expected Results

The app user should have the same permissions for both projects.

Actual Results

The app user only has permissions in the source project. But, not the target project.

Workaround

Have to manually set the permissions for the app user in the target project.