AWS-Transform-Sample.yml

rEC2InstanceAtlassianConfluence:
    Type: AWS::EC2::Instance
    Metadata:
      AWS::CloudFormation::Init:
        configSets:
          bootstrap:
          - security-updates
          - perl-installation
          - psql-tools-installation
          - mount-ebs
          - confluence-installation
          - confluence-modify-serverXML
          - cloudwatch-monitoring-init
        security-updates:
          commands:
            0-write-test-file:
              command: touch ~/security-updates.txt
            1-yum-updates:
              command: sudo yum -y update
        perl-installation:
          packages:
            yum:
              perl-Switch: []
              perl-DateTime: []
              perl-Sys-Syslog: []
              perl-LWP-Protocol-https: []
        psql-tools-installation:
          packages:
            yum:
              postgresql95: []
              postgresql95-devel: []
              postgresql95-libs: []
        mount-ebs:
          commands:
            mount1:
              command: mkfs -t ext4 /dev/xvdf
            mount2:
              command: mkdir /atlassian
            mount3:
              command: mount /dev/xvdf /atlassian
            mount4:
              command: echo "/dev/xvdf      /atlassian   ext4    defaults,nofail        0       2"
                >> /etc/fstab
        confluence-installation:
          packages:
            yum:
              tomcat-native: []
          groups: {}
          users: {}
          sources: {}
          files:
            "/tmp/response.varfile":
              content:
                Fn::Join:
                - ''
                - - "#install4j response file for Confluence 6.0.3\n"
                  - 'launch.application$Boolean=true

'
                  - 'rmiPort$Long=8000

'
                  - 'app.install.service$Boolean=true

'
                  - 'existingInstallationDir=/opt/Confluence

'
                  - 'sys.confirmedUpdateInstallationString=false

'
                  - 'sys.languageId=en

'
                  - 'sys.installationDir=/opt/atlassian/confluence

'
                  - 'app.confHome=/atlassian/application-data/confluence

'
                  - 'executeLauncherAction$Boolean=true

'
                  - 'httpPort$Long=8090

'
                  - 'portChoice=default

'
              mode: '000644'
              owner: root
              group: root
          commands:
            0-write-test-file:
              command: touch ~/confluence-6.0.3-download.txt
            1-download-confluence-6.0.3:
              command: sudo wget https://www.atlassian.com/software/confluence/downloads/binary/atlassian-confluence-6.0.3-x64.bin
              cwd: "/tmp"
            2-make-confluence-6.0.3-executable:
              command: sudo chmod a+x atlassian-confluence-6.0.3-x64.bin
              cwd: "/tmp"
            3-install-confluence-6.0.3:
              command: sudo ./atlassian-confluence-6.0.3-x64.bin -q -varfile response.varfile
              cwd: "/tmp"
          service: {}
        confluence-modify-serverXML:
          packages:
            yum:
              xmlstarlet: []
          commands:
            modifyConf1:
              command: xmlstarlet ed --inplace --insert "/Server/Service/Connector"
                --type attr -n scheme -v https /opt/atlassian/confluence/server.xml
            modifyConf2:
              command: xmlstarlet ed --inplace --insert "/Server/Service/Connector"
                --type attr -n proxyPort -v 443  /opt/atlassian/confluence/server.xml
            modifyConf3:
              command: xmlstarlet ed --inplace --insert "/Server/Service/Connector"
                --type attr -n secure -v true /opt/atlassian/confluence/server.xml
            modifyConf4:
              command: service confluence restart
        cloudwatch-monitoring-init:
          commands:
            0-CloudWatchScriptDownload:
              command: wget -O /tmp/cloudwatch-monitoring.zip https://ec2-downloads.s3.amazonaws.com/cloudwatch-samples/CloudWatchMonitoringScripts-v1.1.0.zip
            1-CloudWatchScriptExtration:
              command: unzip /tmp/cloudwatch-monitoring.zip -d /tmp/
            2-CronPatternDefinition:
              command: echo '*/5 * * * * /tmp/aws-scripts-mon/mon-put-instance-data.pl
                --mem-used --mem-avail --swap-used --disk-space-util --disk-space-used
                --disk-space-avail --disk-path=/ --disk-path=/atlassian'  >>/etc/cron.cloudwatch
            3-CronTabIntegration:
              command: crontab /etc/cron.cloudwatch

To preserve string-encapsulated newlines (eg. '
') with \n, as it appears to be in the source JSON, use

Most readable (with concession to preserving last new line)

"/tmp/response.varfile":
  content:
    !Join
    - '\n'
    - - "#install4j response file for Confluence 6.0.3"
      - 'launch.application$Boolean=true'
      - 'rmiPort$Long=8000'
      - 'app.install.service$Boolean=true'
      - 'existingInstallationDir=/opt/Confluence'
      - 'sys.confirmedUpdateInstallationString=false'
      - 'sys.languageId=en'
      - 'sys.installationDir=/opt/atlassian/confluence'
      - 'app.confHome=/atlassian/application-data/confluence'
      - 'executeLauncherAction$Boolean=true'
      - 'httpPort$Long=8090'
      - 'portChoice=default'
      - ''
  mode: '000644'
  owner: root
  group: root

(terminating newline preserved manually, but if unnecessary this would appear cleaner without it)
To preserve the original's presentation (in code, in addition to the result), use

"/tmp/response.varfile":
  content:
    !Join
    - ''
    - - "#install4j response file for Confluence 6.0.3\n"
      - 'launch.application$Boolean=true\n'
      - 'rmiPort$Long=8000\n'
      - 'app.install.service$Boolean=true\n'
      - 'existingInstallationDir=/opt/Confluence\n'
      - 'sys.confirmedUpdateInstallationString=false\n'
      - 'sys.languageId=en\n'
      - 'sys.installationDir=/opt/atlassian/confluence\n'
      - 'app.confHome=/atlassian/application-data/confluence\n'
      - 'executeLauncherAction$Boolean=true\n'
      - 'httpPort$Long=8090\n'
      - 'portChoice=default\n'
  mode: '000644'
  owner: root
  group: root

The multi-line commands (e.g.

              command: echo '*/5 * * * * /tmp/aws-scripts-mon/mon-put-instance-data.pl
                --mem-used --mem-avail --swap-used --disk-space-util --disk-space-used
                --disk-space-avail --disk-path=/ --disk-path=/atlassian'  >>/etc/cron.cloudwatch

should parse correctly, but are kinda visually troubling due to the --. Just an observation, no action required.