The commit dee41e92f0efac7e453597bed4b4c02f867e3aa9 has introduced a behavior change when adding different cfg files configuring the same configs.
So e.g. when configuring busybox, the default recipe adds a syslog.cfg which enables CONFIG_SYSLOGD=y. So far we had a .bbappend file that adds another .cfg file "disable_syslog.cfg" that changes this to "# CONFIG_SYSLOGD is not set". As the SRC_URI files are now sorted alphabetically, this results in the disable_syslog.cfg being passed to merge_config.sh before syslog.cfg which in the end is not what we intended. We solved it now by doing a SRC_URI_remove in the bbappend, but I'm not sure, if that sorting is causing side effects in other places as well.
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