Use prototype serialization code

[fatherbushido]

The commit in r19147 and r19154 shows issues with serialization of prototype.

Here is a sum up of forum discussions (mainly a leper's investigation).

We have unused prototype serialization code (#407), that should most likely be used (see #1089 for an use for AI deserialization). Though it might be worth considering not making this opt-in (or at least failing loudly if we try to serialize something with an unknown prototype).

The attached diffs are wip, possibly broken and ugly (from leper). It shows the breakage though it seems that the test is incomplete.