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Why is it even running JavaScript? That too for mission critical application.

The mission critical stuff is not JS. Sequences are encoded as JS.

What software on the JWST is not mission critical?

Fair point.

Sequence scripts are written in js.

Execution of sequences, hardware control, resource management, and everything not sequence markup is not. The sequences are not flight software (imho), but the interpreter is.

not defending it, but I think it boils down to the requirement to be able to quickly issue specific commands to various subsystems. So one choice would be a Domain-Specific Language, the other would be an "everyone-already-knows-it" language like JS.

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