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config: apply lua_call privileges before bootstrap

This patch is a bugfix of the `lua_call` runtime access implemented in
commit 38c6b0d38254 ("config: grant runtime access to lua_call from
config").

One of the main reason for runtime privileges is to allow granting guest
user `lua_call` access before the initial bootstrap. During the
implementation of the #10857 in terms of the new behavior of the
supervised failover with the supervised bootstrap strategy it turned out
runtime privileges haven't been added as a first-phase applier making it
impossible to executing some of the lua functions before the initial
bootstrap. This patch fixes it by adding a first-phase applier.

For instance, you might allow guest connection to fetch information on
instances before the bootstrap by configuring `credentials` section like
this.

```yaml
credentials:
  guest:
    privileges:
    - permissions: [ execute ]
      lua_call: [box.info]
```

NO_DOC=see tarantool/doc#4552, added a comment on it

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