This file is indexed.

/etc/mysql/percona-xtradb-cluster.conf.d/isamchk.cnf is in percona-xtradb-cluster-server-5.6 5.6.21-25.8-0ubuntu3.

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#
# The Percona XtraDB Cluster 5.6 configuration file.
#
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

[isamchk]
key_buffer		= 16M