As for your second question, I will simplify the ideas in the sentence this way:
There are military groups (militias) called Ganda Koy in northern Mali. These groups are not part of the government army of the country of Mail. Thus, they are not "official" groups.
If the government of Mali sends its official army to battle, it might use these unofficial militia groups in its effort, or it might not use them.
"It is not clear what role the groups will play." An actor plays a role in a movie. Sometimes, the term "play a role" is used when no movie or acting is involved.
For example, right now, I am playing the role of a teacher while I write this answer. When I ask a question about my Spanish lessons, I am playing the role of a student.
So, will the militia play the role of official army if the country of Mali goes into battle? It is not clear. The writer of the article does not know.