Don't worry about the leaves, Pachypodium tend to drop them in the winter. I don't have a Gracilis, but my Lamerii has lost half its leaves and my Meridionale is completely bare. I gauge their health by how their bodies look rather than the leaves this time of year. I don't have an answer on the watering for you. I generally keep mine in one of those plastic propogation trays for a full year to keep the humidity up a bit as our dry winters always seemed to do in my seedlings before spring.

The same thing has happened to mine. I'll try to post a pic for better observation on my behalf. This is my first time with Morning Glories but I've loved them since I was a child. I started them from a seed using the elementary school method of putting them in a zip lock bag along with a moistened paper towel. They grew to about 1 to 2 inches before I planted them. I unfortunately put them in seed starting potting soil and just came to realize that the pots didn't have any drain holes. Ugh! Therefore by reading your comments I must assume that my soil is just too moistened for these Morning Glories. Thanks for the help!

Tissue culture and they are almost never Blue Java but Namwah.

Sam Marie, all the preceding comments are spot on. But don't give up hope! It's stunted, for sure, and will never be what it might have been, but it's not dead. This looks like a variety that was never meant to be grown in a container all season (and there are some varieties that find that acceptable, just look for "patio tomatoes" and the like), but if you can get hold of the biggest pot you can find and still move around - say 10-15 gallons - and transplant your tomato in there (with a little help from a friend, maybe, to stabilize the top growth during the moving process), you may still get some tomatoes off it. Remove the dying foliage. Leaving it on there will only open a pathway for disease, and there are various kinds of blights that start out looking somewhat like what you've got there, and work their way up the plant, gradually killing it off. I'm not saying this is some kind of blight! Just that it's as well to remove anything unhealthy. And if you find you're removing everything on, say, the bottom 8" of plant so that there's nothing but bare stem down there, go ahead and plant it really deep in its new pot. Brand new roots will spread out from the buried parts of the stems (be sure not to bury any leaves), and your plant may be transformed almost miraculously. I've never done anything like this because I've never had to; and real Tomato Experts on this site might tell me I'm all wet. But if you were to give that plant to me and tell me to do my best with it, that'd be my move. And I'd probably get a 2 cu ft bag of Miracle Gro potting mix, to fill the pot, unless you have something else on hand, preferably "soilless" and meant for container growing. (Yes yes, everyone, I know MG is not everyone's cup of tea. But Sam is fairly new at this. It needs to be easy, I think, and that mix has served me relatively well in quite a variety of situations. I amend as necessary.) In my opinion your having kept this thing going and not looking all that bad, all things considered, in what must be a tiny pot, shows true devotion. You have paid careful attention, to get it this far. Good for you! Now for that biggest possible pot ...