Generator appears to skip some classes in jars

Hopefully reproducible with the following:

```
> wget -O assertj-assertions-generator-2.0.0-unix.zip https://search.maven.org/remotecontent?filepath=org/assertj/assertj-assertions-generator/2.0.0/assertj-assertions-generator-2.0.0-unix.zip
> unzip assertj-assertions-generator-2.0.0-unix.zip
> cd assertion-generator/
assertion-generator> mkdir tmp
assertion-generator> cd tmp
tmp> wget https://jitpack.io/com/github/ga4gh/schemas/d6cc80d/schemas-d6cc80d.jar
tmp> wget http://central.maven.org/maven2/com/google/protobuf/protobuf-java/3.0.0-beta-2/protobuf-java-3.0.0-beta-2.jar
tmp> cd ..
assertion-generator> java -cp "tmp/*:lib/*" org.assertj.assertions.generator.cli.AssertionGeneratorLauncher ga4gh
assertion-generator> find ga4gh/ -type f -name "*.java" | wc -l
9
```

So 9 files have been generated.

```
assertion-generator> rm -rf ga4gh
assertion-generator> cd tmp
tmp> unzip schemas-d6cc80d.jar
tmp> cd ..
assertion-generator> java -cp "tmp:tmp/*:lib/*" org.assertj.assertions.generator.cli.AssertionGeneratorLauncher ga4gh
assertion-generator> find ga4gh/ -type f -name "*.java" | wc -l
143
```

Now 143 files have been generated, which is more what I was expecting.

Is this something really odd with what I'm doing? This looks to me like a bug in how the generator locates classes to generate for.

Comienza en el punto de entrada org.assertj.assertions.generator.cli.AssertionGeneratorLauncher y ejecuta los dos comandos usando schemas-d6cc80d.jar como jar y como directorio descomprimido. Compara el descubrimiento de clases y el número de archivos generados; se considera terminado cuando la forma jar descubre las mismas clases que la forma descomprimida, o cuando la limitación está claramente identificada.

Escrito por el modelo de indexación a partir del texto del issue.