Food is a sacred thing for most any animal (especially for me), so my rule of thumb is never mess with food except to add more things to it every now and then. I expect any dog to be possessive of its food because it's natural. What I do is have my dog hold a down while preparing food, then I send him to the crate, and then he must down of his own accord- I do not tell him this part except for rare occasions. Once he's down, I put down the bowl and close the crate. He now has no worry about losing food. A few times I've went into the crate and added things but I never make it any deal whatsoever- I just open up the door, add stuff, then leave. It's a complete non-issue. I don't correct, I don't praise, I just do and go.
Bones can be a hot topic as well. I'd suggest giving the bone in the crate and allow the dog some time to herself. When she's done, she'll have lost interest in it, then you can let her out. Do not allow her to take the bone with- if she still wants it, she must stay with it in the crate. If she leaves the bone, take it and put it away. You control the resources in this way and there is no fight involved! Plus, if you ever have guests over, especially young ones, you'll have no worries about someone interfering with her bones and risking a confrontation.
To build the trust back, start handfeeding her. Every morsel or handful of food must be earned by obedience. This will teach her that you decide when she eats, you control the food, and she must work for the food. If you keep it fun, she'll also have fun. This is a great bonding experience and it is much better than "give bowl, take bowl, give bowl, take bowl."
Six months is still within the adjustment period. She probably got comfortable enough to try a little challenge just to see where you and her stand in the relationship. Don't let her rattle you! There are MUCH better battles to fight than the one over food; that one usually does more harm than good. Be a strong leader for her throughout daily life and don't let her challenges get to you. Ramp up the obedience and NILIF. Make her move away from you when you walk through the house and not the other way around. Enforce long downs and gradually work up to 30 minutes or longer. Enforce long downs during YOUR mealtime and then feed her afterwards. Make sure she sits and gives you eye contact before you allow her out of doors and be the first one through. Decide when she gets to be petted or have attention and decide how much she gets. Go to an obedience class and make sure to do some fun training at home. Continue to be a strong, fair leader and you will earn her respect, your bond will get stronger, and the speed bumps will lessen and disappear.
If you find things are getting worse, go to the vet and see if there is a medical reason for the growling (pain will contribute to a short temper). After that, find a qualified trainer/behaviorist who can help you see where things are going wrong and how to resolve those problems. Good luck, hang in there!