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Definately 5.3 and up, why? It has integers, bitwise operators, __pairs which is nice for proxy tables. Why "and up"? Well, it has everything Lua 5.3 has and more, but one thing... one thing that bugs me... 5.3 doesn't have %p for string.format :D There's also Moonsharp and recently open sourced Roblox's Luau.
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If you like to bet the future on the probabilities of experimental projects actually coming to fruition, you might also look at Pallene, the experimental sister language to Lua. Pallene is a typed variant of Lua designed to seamlessly interoperate with Lua and C, with the purpose of using type information to compile (AOT) optimized native code for performance. It hopes to somewhat fill the role of LuaJIT with its focus on performance and (hopefully) automatic C bindings.
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Any Lua program over a few kilobytes should use luacheck; if you want to avoid going crazy it's non-negotiable: https://github.com/mpeterv/luacheck You're right that it's a design mistake, but luacheck makes it relatively easy to work around.