There is nothing hard about it, assuming you are using a decent language.
Just add a Crypto<T> type that wraps integers and booleans and that doesn't
allow any non-constant time operations nor implicit conversion to anything that
is not Crypto<T> (which of course means you can't index memory or do branches
based on it).
If the optimizer can screw up things, implement the Crypto<T> operations in
assembly.
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