title: Cloudformation init doesn't execute commands but creates files
body: <p>I am trying to create a couldformation template, and using cfn-init in the same. But I am facing this random issue, where the cfn-init module would run the files and the services configuration perfectly but none of the commands in the commands module is executed. Following is a snippet of my template. </p>
  
  <pre><code>"Metadata": {
      "AWS::CloudFormation::Init": {
        "config": {
          "commands": {
            "cloud": {
              "command" : "whoami &gt;&gt; /home/ubuntu/blah"
            },
            "test" : {
                "command" : "echo \"$MAGIC\" &gt; test.txt",
                "env" : { "MAGIC" : "I come from the environment!" },
                "cwd" : "~",
                "test" : "test ! -e ~/test.txt",
                "ignoreErrors" : "false"
            },
            "test2": {
              "command" : "whoami &gt;&gt; wala",
              "cwd" : "/home/ubuntu"
            }
          },
          "files": {
            "/home/ubuntu/sambhav": {
              "content": {
                "Fn::Join": [
                  "",
                  [
                    "Ok Cool!!!",
                    "\n"
                  ]
                ]
              }
            },
            "/etc/cfn/cfn-hup.conf": {
              "content": {
                "Fn::Join": [
                  "",
                  [
                    "[main]\n",
                    "stack=",
                    {
                      "Ref":"AWS::StackId"
                    },
                    "\n",
                    "region=",
                    {
                      "Ref":"AWS::Region"
                    },
                    "\n",
                    "interval=2",
                    "\n"
                  ]
                ]
              },
              "mode": "000400",
              "owner": "root",
              "group": "root"
            },
            "/etc/cfn/hooks.d/cfn-auto-reloader.conf": {
              "content": {
                "Fn::Join": [
                  "",
                  [
                    "[cfn-auto-reloader-hook]\n",
                    "triggers=post.update\n",
                    "path=Resources.EC2Instance.Metadata.AWS::CloudFormation::Init\n",
                    "action=/usr/local/bin/cfn-init -s ",
                    {
                    "Ref":"AWS::StackId"
                    },
                    " -r EC2Instance ",
                    " --region ",
                    {
                      "Ref":"AWS::Region" 
                    },
                    "\n",
                    "runas=root\n"
                  ]
                ]
              }
            }
          },
          "services" : {
            "sysvinit" : {
              "cfn-hup" : { "enabled" : "true", "ensureRunning" : "true",
                  "files" : ["/etc/cfn/cfn-hup.conf", "/etc/cfn/hooks.d/cfn-auto-reloader.conf"]}
            }
          }
        }
      }
    },
    "Properties": {
      "InstanceType": {
        "Ref": "InstanceType"
      },
      "SecurityGroups": ["staging"],
      "KeyName": {
        "Ref": "KeyName"
      },
      "ImageId": "ami-6.....",
      "Tags" : [
          {"Key" : "Name", "Value" : "Staging"}
      ],
      "UserData" : { 
        "Fn::Base64" : { 
          "Fn::Join" : [
            "", 
            [
              "#!/bin/bash \n",
              "# Install cfn bootstraping tools \n",
              "apt-get update \n",
              "apt-get -y install python-setuptools \n",
              "mkdir aws-cfn-bootstrap-latest\n",
              "mkdir -p /home/ubuntu/work/projects\n",
              "sudo curl https://s3.amazonaws.com/cloudformation-examples/aws-cfn-bootstrap-latest.tar.gz | tar xz -C aws-cfn-bootstrap-latest --strip-components 1 \n",
              "sudo easy_install aws-cfn-bootstrap-latest \n",
              "cp /usr/local/bin/cfn-hup /etc/init.d/cfn-hup \n",
              "chmod +x /etc/init.d/cfn-hup \n",
              "update-rc.d cfn-hup defaults \n ",
              "service cfn-hup start \n",
              "/usr/local/bin/cfn-init --stack ", { "Ref":"AWS::StackName" }, 
              " --resource EC2Instance", " --region ", { "Ref": "AWS::Region" },
              "\n"
            ]
          ]
        }
      }
    }
  </code></pre>