I tried, again and again, to eat from warungs. Always, and I mean ALWAYS got serious diarrhea. Last time I lost 5 kilos in a matter of four days despite drinking plenty of fluids. Ever since, it's proper restaurants, home cooked meals or Domino's for me. Salads and ice aren't really a big issue if you go to places where you spend 100k or more for a meal, because they tend to use drinking water both for cleaning the veggies and making the ice. If in doubt, just ask.
But I have to admit I also don't feel like I'm missing much culinary wise. Sure, I enjoy some Mie Goreng Aceh/Seafood, Sapi Lada Hitam etc. every once in a while at a proper restaurant, but that's about it. Indo food just ain't my thang. Much prefer to go to the many nice restaurants Jakarta and its malls have to offer.