I just upgraded to 5.6.1 and ran the cluster update. i ran into this error but when checking my nodes they are using the the new path method as described. Another thing i notice when my master node changes to a new node the error move to that node.
path.data: /somepath/somedir/data
path.logs: /somepath/somedir/log
Error
Default path settings are removed
This issue must be resolved to upgrade. Read Documentation
Details: nodes with settings: [servername]
Warning
one or more templates use deprecated mapping settings
Resolving this issue is advised but not required to upgrade. Read Documentation
Details: {.monitoring-es=[Coercion of boolean fields], watch_history_3=[Coercion of boolean fields], security-index-template-v6=[Coercion of boolean fields], .monitoring-kibana-2=[Coercion of boolean fields], .monitoring-logstash-2=[Coercion of boolean fields], .watch-history-6=[Coercion of boolean fields], watch_history_2=[Coercion of boolean fields], .monitoring-kibana=[Coercion of boolean fields], security-index-template=[Coercion of boolean fields], .monitoring-logstash=[Coercion of boolean fields], logstash=[The _all meta field is disabled by default on indices created in 6.0, The [include_in_all] mapping parameter is now disallowed], .monitoring-es-2=[Coercion of boolean fields], .ml-anomalies-=[Coercion of boolean fields]}
and i have a 132 of these warn
logstash-2017.08.04
1 warning
The [include_in_all] mapping parameter is now disallowed
Resolving this issue is advised but not required to upgrade. Read Documentation
Details: [[type: syslog, field: @timestamp], [type: syslog, field: @version], [type: default, field: @timestamp], [type: default, field: @version], [type: cisco, field: @timestamp], [type: cisco, field: @version]]