Unable to `git init` because of existig `.git` file

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Steps to reproduce

1. Generate an app using the tool
2. Download and unpack
3. Run git init in the root directory of the app

Expected behaviour

Initializing a Git repository, so you can put the app under version control.

Actual behaviour

$ git init
fatal: not a git repository: /home/[...]/Documents/projects/nextcloud/my-app/../../../.git/modules/nextcloudappstore/scaffolding/my-app

Additional info

The reason the git init command doesn't work, is that the generated app comes with is a .git file that contains the following line:

gitdir: ../../../.git/modules/nextcloudappstore/scaffolding/my-app

If this is not a bug, but intended behavior, maybe someone can explain the reasoning behind this, so I can learn. Also, I would like to know what the recommended way is to put a new app under version control.

Start by inspecting the generated app's .git file and the tool used to generate the app, focusing on why it points to ../../../.git/modules/nextcloudappstore/scaffolding/my-app. Done means establishing and documenting a generation result that can be initialized as a standalone Git repository, or clearly documenting the recommended version-control workflow.