Josephus brings an account of how the Romans conquered Jerusalem, using the Shabbat to their advantage. "And had it not been our practice, from the days of our forefathers, to rest on the seventh day, this bank could never have been perfected, by reason of the opposition the Jews would have made; for though our law gives us leave then to defend ourselves against those that begin to fight with us and assault us, yet does it not permit us to meddle with our enemies while they do any thing else." (AJ 14.63) Josephus then praises the Jews for acting so piously. This passage clearly indicates that on shabbat only direct attacks can be responded to with force, and preparations, such as nuclear sites, terrorist camps, or people not DIRECTLY putting Jews in danger AT THAT MOMENT cannot be attacked. How can we reconcile this with todays operations that happen on Shabbat?

Shalom! You are probably aware that there are many halachic inaccuracies in the writings of Josephus who was not a rabbi, nor any kind of halachic specialist! Nevertheless, it is interesting that in the Book of Maccabees, we find an even more extreme story 200 years beforehand, where Jews refused to even defend themselves on Shabbat and the Greeks utilized this to attack, find them totally passive, and killed more than 1,000 people on one Shabbat! As a result, Matityahu and the halachic authorities then publicized that all Jews must fight on Shabbat. Rav Goren asks, how is it possible that they didn't know beforehand the Oral Tradition, that saving lives supersedes Shabbat! He answers that as we all know, during "Shmad", when the gentiles issue a death penalty to any Jew who observes a particular mitzva, that mitzva takes on a special status and we even must give our lives to observe her (even if not one of the 3 cardinal sins). So when the Greeks (and perhaps the Romans too, in the story you mentioned), proclaimed that Jews must not observe Shabbat, some Jews thought that accordingly, in that generation, they must even give their lives to a special stringent extent, not even defending or, perhaps in the time of Josephus, just doing the minimum defense on Shabbat. This clearly turned out not to be enough, and accordingly was a very serious and tragic mistake, which we would be very unwise to learn from, and that's why the halacha is totally different! Halachically speaking, halachot are decided in the Shulchan Aruch, and there it is clear that even pre-emptive strikes are allowed and obligated on Shabbat, as are any actions of patrolling which deter and prevent any possible danger (see Or. Ch. 330, 6). Even if there is the slightest doubt of a doubt (!) everything is allowed (Yoma 85a). Accordingly, the IDF orders, in conjunction with the Chief Rabbinate, are to correctly prohibit any kind of training or practice, unless it has to do with life-saving issues, in which case it's not only allowed but obligatory. If you are interested in more details, see the many books on the topic of the army and halacha of R. Min-HaHar, R. Ronsky, R. Kaufman, R. Regensberg, R. Avidan and others, where all agree (including all haredi and even anti-Zionist poskim) on this halacha. In addition, one is allowed to stage even an offensive war to liberate the Land of Israel, as did Yehoshua, where the Talmud teaches that he staged the offensive on Shabbat.