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This is not a freeof issue.

It is not that exponentials are "stored as" %e^x, it is that

the expression exp(x) is simplified to %e^x. The function

'exp' just never appears in a simplified expression.

Similarly sin(%i) simplifies to %i*sinh(1). Surely you

don't expect freeof to "find" the sin in %i*sinh(1) or to

"find" the exp in 2^n (which is precisely equivalent to

exp(n*log(2)).

Of course, Maxima is not completely consistent about when it

canonicalizes and when it does not (even when this is

feasible). For example, by default it does *not* simplify

exp(n*log(2)) to 2^n, but to %e^(log(2)*n); it does not

simplify n! to gamma(n+1); etc.