I used to find Popsicle accidentally scratching me or nipping me too hard when playing, but we've bonded well and he likes me, so after I "ouch!"ed a week or so and let him know I wasn't happy (no punishment, just let him know about it), he stopped, and moderates his teething force to gentle nibbles.
If all else fails and you MUST do something about his nails, yeah, FILE them don't cut them:
1. It's safer.
2. Cut nails can have sharp scratchy edges even after cutting. Filed nails are smooth.
3. Lasts longer. Cut nails become sharp as they grow. Filed nails retain smooth tips as they grow.