Using Git on DigitalOcean server: error: The following untracked working tree files would be overwritten by merge

I am using Django for my site on DigitalOcean. So, I had to delete the migration files for one of my apps (accounts) and run makemigrations again. I don’t really recall when or why, but it has caused this error when I pull from origin:

```
$ git pull origin master
From https://github.com/...
...
error: The following untracked working tree files would be overwritten by 
merge:
    accounts/migrations/0001_initial.py
Please move or remove them before you merge.
Aborting  
```

Locally, my accounts app has only one migration:

```
accounts > migrations
__init__.py
0001_initial.py
```

When I run git status on the server, I get a lot of untracked files, and I can see two migrations related to my accounts app (even though locally I only have one migration file in the accounts/migrations) as well as other untracked files (not related to accounts app):

``` 
On branch master
Untracked files:
(use "git add <file>..." to include in what will be committed)
    accounts/migrations/0001_initial.py
    accounts/migrations/0002_alter_user_id.py
    ...
```

Given that I don’t want to mess with the production database, I don’t wish you to change the migration files on the server to replicate the local migration files unless this does not cause any problem for my server. So, how should I resolve this error?