"ERROR: File xxx can't be indexed twice." when analyzing a solution with a mix of C# and C++

Below is my Azure pipeline to analyze a solution with a mix of C# and C++.

This is the error of executing the project build command:

> ERROR: Error during SonarScanner execution ERROR: File
> HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/App.config can’t be
> indexed twice. Please check that inclusion/exclusion patterns produce
> disjoint sets for main and test files

How can I resolve this error?

Logs: build command execute log

resources:
  repositories:
  - repository: Dependency
    type: githubenterprise
    endpoint: https://github.azc.ext.xxx.com
    name: cloud-client/Dependency

trigger: none

pool: 'SWindows2022-DEV'

variables:
  buildPlatform: 'x64'
  buildConfiguration: 'Release'

steps:
- checkout: self
- checkout: Dependency

- script: |
     move Dependency/KHPLib $(Build.SourcesDirectory)

- task: NuGetToolInstaller@1


- task: PowerShell@2
  inputs:
    targetType: 'inline'
    script: |
      Invoke-WebRequest -Uri 'https://sq.corp.xxxcloud.net/static/cpp/build-wrapper-win-x86.zip' -OutFile 'build-wrapper.zip'
      Expand-Archive -Path 'build-wrapper.zip' -DestinationPath '.'
      Invoke-WebRequest -Uri 'https://github.com/SonarSource/sonar-scanner-msbuild/releases/download/5.13.0.66756/sonar-scanner-msbuild-5.13.0.66756-net46.zip' -OutFile 'sonar-scanner-msbuild.zip'
      Expand-Archive -Path 'sonar-scanner-msbuild.zip' -DestinationPath './SonarScanner'

- task: VSBuild@1
  inputs:
    solution: 'KHPLib\src\KHPLib\KHPLib.vcxproj'
    platform: '$(buildPlatform)'
    configuration: '$(buildConfiguration)'

- task: SonarQubePrepare@5
  inputs:
    SonarQube: 'https://sq.corp.xxxcloud.net'
    scannerMode: 'CLI'
    configMode: 'manual'
    cliProjectKey: 'xxx_HPCEMConnectionWizardWin'
    cliSources: '.'
    extraProperties: |
      sonar.cfamily.build-wrapper-output=bw-output
      sonar.java.file.suffixes=-

- task: CmdLine@2
  inputs:
    script: |
      SonarScanner\SonarScanner.MSBuild.exe begin /k:"xxx_HPCEMConnectionWizardWin" /n:"HPCEMConnectionWizardWin\HPCEMConnectionWizardWin.sln" /v:"1.0" /d:sonar.cfamily.build-wrapper-output="bw-output"
      build-wrapper-win-x86\build-wrapper-win-x86-64.exe --out-dir bw-output "C:\Program Files\Microsoft Visual Studio22\Enterprise\MSBuild\Current\Bin\MSBuild.exe" HPCEMConnectionWizardWin\HPCEMConnectionWizardWin.sln -t:Rebuild /p:configuration=release /p:platform=x64
      SonarScanner\SonarScanner.MSBuild.exe end

- task: SonarQubeAnalyze@5

- task: SonarQubePublish@5
  inputs:
    pollingTimeoutSec: '300'

- task: sonar-buildbreaker@8
  inputs:
    SonarQube: 'https://sq.corp.xxxcloud.net'

<hr/>

Update 2023-05-27

I updated the following pipeline task:

- task: SonarQubePrepare@5
  inputs:
    SonarQube: 'https://sq.corp.xxxcloud.net'
    scannerMode: 'CLI'
    configMode: 'manual'
    cliProjectKey: 'xxx_HPCEMConnectionWizardWin'
    cliSources: '.'
    extraProperties: |
      sonar.cfamily.build-wrapper-output=bw-output
      sonar.java.file.suffixes=-
      sonar.verbose=true
      sonar.sources=HPCEMConnectionWizardWin/src/,HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/Model/,HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/View/,HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/ViewModel/

New error:

> ERROR: Error during SonarScanner execution
2023-05-27T12:25:22.4759667Z File HPCEMConnectionWizardWin/src/HPCEMConnectionWizardLauncher/framework.h can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files

Here is the code I like to analyze:

The C# code (*.cs) directory lists:

• HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/Model/
• HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/View/
• HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/ViewModel/

The C++ code (.cpp,.h) directory lists:

• HPCEMConnectionWizardWin/src/

Verbose log: https://community.sonarsource.com/uploads/short-url/pANjC2FqXe3iqumr095tLL1TmLx.txt

You need to check if HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/App.config is included twice somehow. You should add sonar.verbose=true in the SonarQubePrepare step and check what files are indexed by Sonar. Then you can see where the duplication lies. Next, follow Narrowing the Focus to make sure certain files are not indexed twice.

For a quick workaround, just exclude that HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/App.config file with:

sonar.exclusions= HPCEMConnectionWizardWin/HPCEMConnectionWizardWin/App.config