When adding a file from a branch or local folder (source) to another branch (target) not having the file, use its location in the source as the location in the target.

Currently all new files are placed in the default folder [1].

Let's assume a new file, "HelloWorld.cls", in the source is located in .../force-app/main/default/classes/special/ and that class doesn't exist in the target. When the deployment is complete the file should exist in the target's .../force-app/main/default/classes/special/ folder, matching its location in the source. Currently it would be placed in .../force-app/main/default/classes/.

[1] https://docs.gearset.com/en/articles/2835001-structuring-your-source-control-repository