Maintain git repo inside another git repo

I have always used symlinks to maintain two separate and distinct repos.

You can use a .gitignore file in the parent A repository (ignoring B), but firstly making sure that the B repository is not currently being tracked: commit the parent .gitignore before adding the second B repository.

It sounds like you want to use Git submodules.

Git addresses this issue using submodules. Submodules allow you to keep a Git repository as a subdirectory of another Git repository. This lets you clone another repository into your project and keep your commits separate.

Yes, you can do exactly what you're asking with the file hierarchy you drew. Repo-B will be independant and have no knowledge of Repo-A. Repo-A will track all changes in it's own files and Repo-B's files.

However, I would not recommend doing this. Every time you change files and commit in Repo-B you'll have to commit in Repo-A. Branching in Repo-B will mess with Repo-A and branching in Repo-A will be wonky (trouble removing folders, etc.). Submodules are definitely the way to go.