Here I will try to include the arguments passed to each script for comprehensiveness purposes. Also when a script is highlighted it means that all the scripts under that highlighted script are executed within the highlighted script.
Additionally, not all of these scripts are going to be run each time /scripts/upcp is executed. Whether each one is executed or not depends on many different factors which we will not be discussing here. The purpose of this guide is only to show you what scripts are expected to be executed when /scripts/upcp is running.
/scripts/upcp
'/usr/local/cpanel/scripts/upcp'
'/usr/local/cpanel/scripts/gather-update-logs'
'/usr/local/cpanel/scripts/hook'
'/usr/local/cpanel/scripts/hook', '--category=System', '--event=upcp', '--stage=post'
'/usr/local/cpanel/scripts/hook', '--category=System', '--event=upcp', '--stage=pre'
'/usr/local/cpanel/scripts/maintenance', '--log=' . $logfile_path, '--pbar-start=20', '--pbar-stop=95'
'/usr/local/cpanel/scripts/maintenance', '--post', '--log=' . $logfile_path, '--pbar-start=55', '--pbar-stop=95'
'/usr/local/cpanel/scripts/maintenance', '--pre', '--log=' . $logfile_path, '--pbar-start=20', '--pbar-stop=30'
'/usr/local/cpanel/scripts/post_sync_cleanup', '--log=' . $logfile_path, '--pbar-start=30', '--pbar-stop=55'
'/usr/local/cpanel/scripts/postupcp'
'/usr/local/cpanel/scripts/preupcp'
'/usr/local/cpanel/scripts/try-later'
'/usr/local/cpanel/scripts/upcp'
'/usr/local/cpanel/scripts/upcp', @retain_argv, '--fromself'
'/usr/local/cpanel/scripts/upcp-running'
'/usr/local/cpanel/scripts/updatenow', "--log=$logfile_path", '--checkremoteversion'
'/usr/local/cpanel/scripts/updatenow', '--upcp'
/usr/local/cpanel/scripts/maintenance
'/usr/local/cpanel/scripts/link_3rdparty_binaries'
'/usr/local/cpanel/scripts/rdate'
'/usr/local/cpanel/scripts/find_outdated_services --auto'
'/usr/local/cpanel/scripts/checkccompiler'
'/usr/local/cpanel/bin/migrate_all_feature_lists_to_current'
'/usr/local/cpanel/scripts/mainipcheck'
'/usr/local/cpanel/scripts/update_neighbor_netblocks'
'/usr/local/cpanel/scripts/update_known_proxy_ips'
'/usr/local/cpanel/scripts/check_valid_server_hostname --notify'
'/usr/local/cpanel/scripts/checkusers'
'/usr/local/cpanel/scripts/vzzo-fixer'
'/usr/local/cpanel/scripts/quota_auto_fix'
'/usr/local/cpanel/scripts/clear_orphaned_virtfs_mounts --inactiveonly'
'/usr/local/cpanel/scripts/disable_prelink'
'/usr/local/cpanel/scripts/cleanquotas'
'/usr/local/cpanel/scripts/autorepair autorepair'
'/usr/local/cpanel/scripts/purge_old_config_caches'
'/usr/local/cpanel/scripts/cleansessions'
'/usr/local/cpanel/scripts/checkbashshell'
'/usr/local/cpanel/scripts/dnsqueuecron'
'/usr/local/cpanel/scripts/rebuild_whm_chrome'
'/usr/local/cpanel/bin/checkallsslcerts --allow-retry --verbose'
'/usr/local/cpanel/scripts/check_domain_tls_service_domains.pl --prune'
'/usr/local/cpanel/scripts/clean_up_temp_wheel_users'
'/usr/local/cpanel/scripts/findphpversion'
'/usr/local/cpanel/scripts/listcheck'
'/usr/local/cpanel/scripts/updateuserdomains'
'/usr/local/cpanel/bin/empty_user_trash --quiet --all'
'/usr/local/cpanel/bin/empty_user_horde_temp_files --quiet --all'
'/usr/local/cpanel/scripts/build_maxemails_config'
'/usr/local/cpanel/scripts/updateuserdatacache --force'
'/usr/local/cpanel/scripts/check_maxmem_against_domains_count --always-fix'
'/usr/local/cpanel/scripts/resetmailmanurls'
'/usr/local/cpanel/scripts/mysqlconnectioncheck'
'/usr/local/cpanel/bin/postgrescheck --check-auth --reset-pass-on-fail'
'/usr/local/cpanel/scripts/chkpaths'
'/usr/local/cpanel/scripts/hackcheck'
'/usr/local/cpanel/scripts/oopscheck'
'/usr/local/cpanel/scripts/fixetchosts'
'/usr/local/cpanel/scripts/check_unreliable_resolvers --notify'
'/usr/local/cpanel/bin/is_script_stuck --script=autossl_check --time=22h --kill --notify=root'
'/usr/local/cpanel/scripts/quotacheck'
'/usr/local/cpanel/scripts/email_archive_maintenance'
'/usr/local/cpanel/scripts/email_hold_maintenance'
'/usr/local/cpanel/scripts/expunge_expired_certificates_from_sslstorage'
'/usr/local/cpanel/scripts/notify_expiring_certificates'
'/usr/local/cpanel/scripts/notify_expiring_certificates_on_linked_nodes'
'/usr/local/cpanel/scripts/expunge_expired_transfer_sessions'
'/usr/local/cpanel/scripts/expunge_expired_pkgacct_sessions'
'/usr/local/cpanel/scripts/smartcheck'
'/usr/local/cpanel/scripts/compilerscheck'
'/usr/local/cpanel/scripts/check_mount_procfs'
'/usr/local/cpanel/scripts/setup_modsec_db'
'/usr/local/cpanel/scripts/modsec_vendor update --auto'
'/usr/local/cpanel/bin/check_cpstore_in_sync_with_local_storage'
'/usr/local/cpanel/scripts/compilers restore'
'/usr/local/cpanel/scripts/dovecot_maintenance --background'
'/usr/local/cpanel/bin/clean-datastores --background root'
'/usr/local/cpanel/scripts/spamassassin_dbm_cleaner'
'/usr/local/cpanel/scripts/check_security_advice_changes --notify --background'
'/usr/local/cpanel/bin/dcpumon --killproc'
'/usr/local/cpanel/bin/setupdbmap'
'/usr/local/cpanel/bin/fix_userdata_perms'
'/usr/local/cpanel/scripts/detect_env_capabilities'
'/usr/local/cpanel/scripts/manage_greylisting --init --update_common_mail_providers'
'/usr/local/cpanel/scripts/migrate_local_ini_to_php_ini --run --verbose'
'/usr/local/cpanel/scripts/check_mysql',
'/usr/local/cpanel/bin/refresh_plugin_cache'
'/usr/local/cpanel/scripts/ccs-check --run --ssl'
'/usr/local/cpanel/scripts/perform_sqlite_auto_rebuild_db_maintenance'
'/usr/local/cpanel/scripts/vps_optimizer'
'/usr/local/cpanel/bin/purge_dead_comet_files --quiet'
'/usr/local/cpanel/scripts/rpmup'
'/usr/local/cpanel/scripts/process_pending_cpanel_php_pear_registration'
'/usr/local/cpanel/scripts/sysup'
'/usr/local/cpanel/scripts/find_and_fix_rpm_issues'
'/usr/local/cpanel/scripts/updatesigningkey'
'/usr/local/cpanel/bin/cloudlinux_update'
'/usr/local/cpanel/scripts/mkwwwacctconf'
'/usr/local/cpanel/scripts/fixrndc -f'
'/usr/local/cpanel/scripts/fixrndc'
'/usr/local/cpanel/scripts/check_cpanel_rpms'
'/usr/local/cpanel/scripts/ftpquotacheck'
'/usr/local/cpanel/scripts/restartsrv mysql'
'/usr/local/cpanel/scripts/purge_modsec_log'
'/usr/local/cpanel/scripts/buildeximconf --no_chown_spool'
'/usr/local/cpanel/scripts/restartsrv_eximstats'
'/usr/local/cpanel/scripts/litespeed-check --run'
'/usr/local/cpanel/scripts/jetbackup-check --run'
'/usr/local/cpanel/bin/wpt_license --download'
/usr/local/cpanel/scripts/try-later
'/usr/local/cpanel/scripts/cpservice'
Note: The following scripts are usually part of the cPanel hook system so as a result they are executed only when there are already custom scripts configured to be run during the upcp through the hook system:
'/usr/local/cpanel/scripts/hook'
'/usr/local/cpanel/scripts/postupcp'
'/usr/local/cpanel/scripts/preupcp'
So these three could also execute other extra scripts, depending on what has been hooked to them.
You can refer to this link for more information on how hooks work in cPanel:
https://documentation.cpanel.net/display/DD/Guide+to+Standardized+Hooks