OH NO!

My thyme plant has a lot of blossoms but it is very spindly. I better amend the soil---just wait til you see the next picture. And I'm wondering where all the bees are! I want to do a flagstone path around the shop and fill in-between with thyme (mother-of-thyme?) plants and never did because of the bees. I won't have to worry about that now, will I?Here is that other picture I mentioned above! What a sorry sight. This is really a tomato plant.
All there is is a stem and a yellowed leaf and a tomato. I wonder if it is safe to eat! I planted 4 tomato plants in this garden and 2 look like this. The other 2 look a little better but not much. I'm wondering if the mulch I put on is too strong. We got a huge load of horsemanure that has wood chips mixed in. Maybe it needs to age more. We have had the manure for a good 9 months now, and I thought that would be enough aging time. Oh well, garden and learn---I always say!