Proof.
This is formal. Proof of (1). Let T = \mathop{\mathrm{lim}}\nolimits _{i \in I} T_ i be the directed limit of affine schemes T_ i over S. We will prove that the functor \mathop{\mathrm{colim}}\nolimits \mathcal{X}_{T_ i} \to \mathcal{X}_ T is essentially surjective. Recall that an object of the fibre product over T is a quadruple (T, x, z, \alpha ) where x is an object of \mathcal{X} lying over T, z is an object of \mathcal{Z} lying over T, and \alpha : p(x) \to q(z) is a morphism in the fibre category of \mathcal{Y} over T. By assumption on \mathcal{X} and \mathcal{Z} we can find an i and objects x_ i and z_ i over T_ i such that x_ i|_ T \cong T and z_ i|_ T \cong z. Then \alpha corresponds to an isomorphism p(x_ i)|_ T \to q(z_ i)|_ T which comes from an isomorphism \alpha _{i'} : p(x_ i)|_{T_{i'}} \to q(z_ i)|_{T_{i'}} by our assumption on \mathcal{Y}. After replacing i by i', x_ i by x_ i|_{T_{i'}}, and z_ i by z_ i|_{T_{i'}} we see that (T_ i, x_ i, z_ i, \alpha _ i) is an object of the fibre product over T_ i which restricts to an object isomorphic to (T, x, z, \alpha ) over T as desired.
We omit the arguments showing that \mathop{\mathrm{colim}}\nolimits \mathcal{X}_{T_ i} \to \mathcal{X}_ T is fully faithful in (2).
\square
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