eb CLI won't download logs files from /var/log after setup amazon cloudwatch agent

Question

I recently configured the Amazon CloudWatch Agent by adding lines to an .ebextensions file

files:
  "/tmp/custom-cloudwatch-config.json":
    mode: "000600"
    owner: root
    group: root
    content: |
      {
        "logs": {
          "logs_collected": {
            "files": {
              "collect_list": [
                {
                  "file_path": "/var/log/app-logs/*.log",
                  "log_group_name": "`{"Fn::Join":["/", ["/aws/elasticbeanstalk", { "Ref":"AWSEBEnvironmentName" }, "var/log/app-logs"]]}`",
                }
              ]
            }
          }
        }
      }

container_commands:
    01_append_logs_config:
        command: amazon-cloudwatch-agent-ctl -a append-config -m ec2 -s -c file:/tmp/custom-cloudwatch-config.json

After deploying this configuration file, I lost access to common log files that I previously obtained when running the command eb logs -a , such as cfn-init.log, cfn-init-cmd.log, messages, web.stdout.log, and others.

It appears that this configuration file may have overridden some default settings. I would like to back to previous behavior where I got these files