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This is a very interesting topic in grammar. Based on Folwer, "what are" is a better choice here. Here is what Fowler says in his Modern English Usage:

2. Singular what: A problem of singular or plural verb agreement arises when what is singular but looks forward to a plural noun or pronoun later in the sentence: What we need is/are clear guidelines. Fowler had a useful rule that if the sentence begins in the singular (i.e. the initial what is singular), the continuation should also be singular; so the example just given would be expressed in the form What we need is clear guidlines. In current use, this rule is often respected, as the following examples show: What really worries me is the numbers - Nina Bawden, 1987 / What bothered him was drivers who switched lanes without signaling - New Yorker, 1989. In these cases, it is arguable that a noun phrase such as the fact of should be understood after the main verb; it is not the numbers or drivers as such that cause the worry in the first example or bother in the second, but the fact of what they represented or were doing.

3. Plural what: A different situation arises when what is plural: I have few books, and what there are do not help me. In this sentence, what refers back to books, and so its plural status is clear. When what refers forward, the choise is less obvious: We seem to have abandoned what seem/seems to us to be the most valuable parts of our Constituition. Fowler (whose example this is) had another useful rule in these cases: If what can be resolved into the -s, with -s standing for a plural noun that comes later in the sentence, the construction should be plural. In the example just given, what can be resolved into the parts of our Constituition that ..., and the continuiation should therefore be seem (plural), not seems. If the relative clause introduced by what comes at the head of the sentence, the same rule can be followed if what can be resolved into that which: What [that which] is required is faith and confidence, and willingness to work. This principle is much less secure, however, since what in the example given can easily be resolved as the things which (plural): What [the things which] are required are faith and confidence, and willingness to work. Here clearly there is a chioce, and naturalness and rhythm will often be decisive; the important point is that the choice between singular and plural should be consistent throughout the sentence, and that a singular what should not be followed by a plural continuation: *What is required are faith and confidence, and willingness to work.
quote:
We seem to have abandoned what seem/seems to us to be the most valuable parts of our Constituition.


This example of Fowler's is actually close to your "The encoded meanings are semantic meanings and are what are described in dictionaries and grammar books."
First of all, "what" is not at the head of the sentence, second, "what" could be resolved as "the meanings which", so the plural is the better chioce.

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