Missing dependencies of extensions should not prevent execution

[akerbos]

Currently, some extensions specify essential dependencies. While they are essential to their own execution, they are not for the whole program. For example, missing gnuplot does not prevent most documents from being compiled.

1. Separate dependencies by source; only dependencies of the core should always block execution.
2. Check core dependencies and what can be figured out from CLI parameters at startup.
   For example, engine and log mode are known then.
3. Check extension dependencies when they are to be run. Don't abort everything; just skip the extension.

On a side-note, dependencies from engines don't seem to show up in the --dependencies dump?