Convert all File stuff to Path; add fallback to Config from DistConfig when required

This was done to convert all remaining `File`-specific stuff to using `Path`. That is necessary because we have to support Hadoop file systems (HDFS etc.) equally well - already discussed.

As for this particular change, I personally feel this is getting pretty ugly because the client code is having to juggle between DistConfig and Config when it comes to dealing with `mappingsDir`, 'ontologyFile` and `dumpDir`. But this is supposed to be handled behind-the-scenes by the config object.

I propose to reject this PR and combine Config and DistConfig into one single DistConfig. I'll make a new PR. Here's how DistConfig will look like:

```scala
/**
 * Class for distributed configuration
 */
class DistConfig(configProps: Properties, config: Config)
{
    // add all Spark and Hadoop-specific stuff

   // dumpDir, mappingsDir, ontologyFile => do the fallback to config logic here and delegate to config accordingly.

   // for the rest of the config.* methods, simply delegate. Act as wrapper.

}
```