Please read How do I post a question effectively?. There is a lot of material in your post that, by your own admission, is not pertinent to the issue you are experiencing. It also doesn't help that we can't easily replicate your issue because of the lack of input.

Regardless, I suspect your issue is that:

$file_content[$u] = s/logo-$source_branch/logo-$cloneName/g ;

should read

$file_content[$u] =~ s/logo-$source_branch/logo-$cloneName/g ;

See Binding Operators if you are unsure why.