Food

I have the same problem. No food on any planet, low morale. No farms, nothing in the tech tree to indicate farming, and I can't find anything with instructions on how to develop food. Is there a new manual for the game?

If you play carbon-based, you are at a severe disadvantage at the moment. While aquatic can build their special farms anywhere and the other two don't need food at all, carbon-based has to rely on finding arable land tiles in order to get food.

In singleplayer it's not quite that bad though. There is the Galactic Wonder Kimberly's Refuge (the AI seems to not want it so you can always get it), which you should build ASAP on your best food planet. Use adjacency bonuses (from arable/farms, colonial hospitals, cities and colony capitals) to significantly boost Kimberly's food output. Then assign farmer citizens to the planet you built it on. This way you can build enough cities to pop-max at least your homeworld and a few key worlds (i.e. your best planets). There is also a tech that gives +1 food to all your planets.

Morale:

It has become harder now to keep your people happy (introduction of tax rate in 3.0 and its accompanying morale penalty, introduction of colony limit in Intrigue). I suggest to build morale improvements immediately on your colonies after the initial manufacturing-enhancing buildings, so that you can increase tax rate. At the very beginning, you can set tax rate to 0 to help with morale (if you don't play a Content race), it doesn't give much money early-on anyway. Also, research morale-boosting tech (e.g. "Easy to Please" tech!) and make heavy use of mercs and government ships that boost the morale of the planet they get stationed at. There are also celebrities and leaders.

In the long term, it should be your goal to get both 100% approval and 100% tax rate (or whatever rate you're comfortable with roleplay-wise) on all of your planets.

Thanks for the advice, but it seems that I am still unable to build farms. I haven't yet seen an arable tile or a function to build one either. I just did a file verification, thinking that perhaps my program was missing something. It did say 3 files were updated, and so trying again, but finding the same 0 food issue. I'll see about building the Kimberly's Refuge next.

This can absolutely happen if you are unlucky with the planets in your corner of the galaxy. When mousing over planets on the galaxy map, it shows "Food" if they have arable tiles on them (in the same way as for rare resources).

For Kimberly's Refuge you don't necessarily need food tiles on the planet, just use the adjacency bonuses as good as you can.

Got it now.

NO. 

Farms haven't disappeared so much as been restructured. When your planets have arable land they will generate a set amount of food without improvement. If you build a farm on the arable land it gives you a nice boost.

but there aint any farms

I'm on Intrigue 3.01 and I see farms.  You just upgrade arable land to a farm.

Farms are very much still in the game, but you have to build them on arable land now. If you have a planet without arable land it won't give you the option to build a farm. 

I guess what he meant is that he can't find any arable land. Honestly it's ridiculous to depend so much on RNG to know if you can grow your population or not. There are tons of +growth techs that give you basically no benefit if you don't find enough arable land. On top of that you have ridiculous situations like "Bread basket" planets and such spawning without any arable land. So yeah, your bread basket produces a whopping maximum of... Zero food.

Right now carbon-based races are basically unplayable, unless you like gambling.