MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process failed.
mysql:5.6 fail to start with gtid_mode=on configuration.
mysql:5.6 fail to start with gtid_mode=on settings.
      Sep 16, 2015
          
This is the command used to start the container:
  docker run --name mysql-master -d \
    -m 2g \
    -e MYSQL_ROOT_PASSWORD=rootpassword \
    -e MYSQL_DATABASE=example \
    -p 3307:3307 \
    mysql-test # <- the image built from the above Dockerfile
          
I finally was able to test this and it looks like you need a log_slave_updates = TRUE in your conf file.

When I ran with your config I found that the error was a little higher up in the log:
2015-10-09 22:17:10 235 [ERROR] --gtid-mode=ON or UPGRADE_STEP_1 or UPGRADE_STEP_2 requires --log-bin and --log-slave-updates
2015-10-09 22:17:10 235 [ERROR] Aborting
Here is the conf file I used:
[mysqld]
server_id    = 1
port         = 3307
report_host  = 172.17.42.1
report_port  = 3307
general_log      = ON
general_log_file = /var/log/mysql/queries.log
log_bin          = /var/log/mysql/mysql-bin.log
# used /var/log/mysql so that I didn't have to mkdir or chown
binlog_do_db     = chaostesting
log_slave_updates = TRUE
master_info_repository   = TABLE
gtid_mode                = ON
enforce_gtid_consistency = ON
And my docker run:
$ docker run -it --rm --name mysql \
  -v "$PWD"/master.cnf:/etc/mysql/conf.d/master.cnf:ro \
  -e MYSQL_ROOT_PASSWORD=rootpassword \
  -m 2g -e MYSQL_DATABASE=example \
  -p 3307:3307 \
  mysql