This is going to be necessary. The warmth of the tropics processes out organic material so fast, the mulch from your alley trees will not be sufficient to maintain fertility. So you will need cover crops in between to bump organic content back up--especially since you plan on harvesting BOTH vegetable produce and animal bio-mass from this system. You're expecting a lot from it, so you'll need to do so only on a every-other-year sort of cycle, or maybe even one out of three years. This isn't hard, just partition your land up into thirds and harvest one third a year. This is actually a benefit: you get to concentrate on the biggest bang for your buck on a smaller plot. It's basically rotational gardening.
Because it's a tropical setting, with moisture available all year, this can be a continuous system, although I might want to break it up with buckwheat or some other cover crop occasionally, to prevent problems with disease. Buckwheat can be used for a short rotation, or sweet potatoes for a long rotation.