Fix examples and annotations on Flux command implementations

With the Flux validator in the Metafacture IDE, the `@In` and `@Out`
annotations on the Flux command implementation classes are processed
to check the workflows (see [1]). With the current Flux examples in
metafacture-core, the IDE reports some errors and warnings which
this commit fixes:

- Update morph-marc21.flux to use the new `encode-literals` command
- Fix `@In` and `@Out` annotations of `TripleCount`
- Add some missing `@In`, `@Out`, and `@Description` annotations

[1] https://github.com/culturegraph/metafacture-ide/pull/23