The SFDX standard file folder structure can be customized by modifying the sfdx-project.json file that is located in your Git repository source files folder hierarchy. The project configuration file sfdx-project.json configuration file indicates that the directory is a Salesforce DX project. According to the Salesforce documentation on this topic, "The configuration file contains project information and facilitates the authentication of orgs and the creation of second-generation packages. It also tells Salesforce CLI where to put files when syncing between the project and org."

Note the location of the sfdx-project.json file in Bitbucket (as an example) in the screenshot below:

See the following Salesforce documentation links for further details on how to edit your sfdx-project.json configuration file:

https://developer.salesforce.com/docs/atlas.en-us.sfdx_dev.meta/sfdx_dev/sfdx_dev_ws_config.htm