Running the controller via VSCode uses different paths for configs/stores/etc. which leads to some problems

Description

The problmes include:

• [] duplicated config files which all need to be put into gitignore
• [] the controller run via vscode uses a different place to store configs and overwrites the used one. This leads to an issue with saving the correct configuration because it gets overwritten all the time. Example: change security to secure, when starting the controller via vscode it gets changed back to insecure and starts in this mode