cfn-lint -iW causes template metadata to be ignored

[ispyinternet]

CloudFormation Lint Version

cfn-lint 1.20.0

What operating system are you using?

Amazon Linux 2

Describe the bug

I have the following metadata:

Metadata:
  cfn-lint:
    config:
      ignore_checks:
        - E3006

Expected behavior

if I run cfn-lint template.yaml I only see the warnings
if I run cfn-lint -iW template.yaml I still get the E3006 error

Reproduction template

AWSTemplateFormatVersion: '2010-09-09'
Transform: 'AWS::Serverless-2016-10-31'
Metadata:
  cfn-lint:
    config:
      ignore_checks:
        - E3006
        
Resources:
  GoogleClientSecret:
    Type: AWS::SSM::Parameter::Value<String>
    Properties:
      Name: "/ClientSecret"

[dishikang123]

@ispyinternet see #3816. We have the same issue.

[kddejong]

By default the CLI parameters will override any other configuration. So it will ignore Metadata and .cfnlintrc file configurations. There is an option to add --merge-configs to merge lists.

cfn-lint -iW --merge-configs -- local/issue/3839.yaml will return no errors.