Before accessing the main application, the user must log in to our application with our users who have nothing to do with atlassian stuff. But due to atlassian settings, my security configurations are not working. In particular, the default spring security functionality does not work.
I had the same issue, and ended up disabling the AutoConfiguration for the Atlassian Spring Boot configuration and override the configuration provided in AtlassianConnectWebSecurityConfiguration I also dropped a lot of the other out-of-the-box configuration, so maybe you can ‘simply’ create a new WebSecurityConfiguration that has a higher priority then the one provided by the Atlassian Starter which is at SecurityProperties.BASIC_AUTH_ORDER + 1