Repository A)
MAIN
../repository_A/
../repository_A/some_directory/some_files
Repository B)
MAIN
../repository_B/
../repository_B/SRC/some_directory/some_files
The repository_B structure is identical to the repository_A structure,
 except for the /SRC/ directory which is in place because the main directory of repository_B has a .gitmodules file.
The ultimate goal is to clone/merge the content of /repository_B/SRC/ directory into /repository_A/ root - the folder structure is identical, so we need to write into existing folders of repository_A - for example write content of repository_B/SRC/includes directory into repository_A/includes.
Behind the task is that i have a modular system which is repository_A that is extended through modules which are represented by repository_B.
Another option that would do the job too would be to mv repository_A into another directory so that the folder structure is identical to repository_B.
 
    