How to manipulate directories using Python
Enumerate

counter = 1
for repo in git_repo_tags:
  # ...
  print('--Removing the .git folder ' + str(counter) + '/8')
  counter += 1


should be using enumerate:

for counter, repo in enumerate(git_repo_tags, start=1):


String interpolation

print('--Removing the .git folder ' + str(counter) + '/8')


can be

print(f'--Removing the .git folder {counter}/{len(git_repo_tags)}')


The 8 should not be hard-coded.

Pathlib

For basically every one of your directory and file names, and many of your file operations (rmtree being an exception), you should consider using pathlib.Path. For instance, this:

if not os.path.exists('Food-101/images'):
    os.makedirs('Food-101/images')
    print('Created the Food-101/images')


can be

image_path = Path('Food-101/images')
if not image_path.exists():
    image_path.mkdir(parents=True)
    print(f'Created {image_path}')


Path parsing

Rather than this:

name_of_folder = line.split('/')[0]
name_of_file = line.split('/')[1].rstrip()


consider at least unpacking it, i.e.

folder_name, file_name = line.rsplit('/', 1)


But it's better to again use pathlib:

line_path = Path(line)
folder_name = line_path.parent
file_name = line_path.name


Functions

Move logically-related chunks of code to subroutines for better legibility, maintainability, modularity, testability, etc.

Indentation

Use four spaces, which is more standard. You do this in some places but not others.