In GitHub Enterprise Server 3.10 and later, the requirements for TLS security levels have changed due to an upgrade to containers in the underlying OS. On an instance with a GitHub Advanced Security license and secret scanning enabled, dry runs sometimes incorrectly reported no results for custom patterns. On an instance with multiple nodes, ghe-spokes status did not identify Git replicas in certain incomplete states, causing a false report that replication was in sync and leading to data loss or replication issues during failover. On an instance with a GitHub Advanced Security license and secret scanning enabled, secret scanning suggested incorrect filters when viewing both open and closed alerts. Repository exports using ghe-migrator or the REST API's operation for organization migrations could fail when a large number of commit comments or long commit comments were present.

In some cases, this led to data loss during failover. Ghe-repl-status did not identify Git replicas in certain incomplete states and incorrectly suggested that a failover could be performed safely.

On an instance in a cluster configuration, when managing maintenance mode using ghe-cluster-maintenance, an erroneous warning appeared that read 'Warning: Maintenance mode set on primary, please make sure to set it on any active replica if needed'. var/log/lastlog was not copied over as a sparse file during ghe-upgrade, which could cause issues by using additional disk space. Multiple lines in babeld logs could run together, making it unclear to administrators if the operations were related. When a site administrator ran ghe-btop via SSH, the command did not run and a /usr/bin/env: python3: No such file or directory error occurred.

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