Remove API doc links from reindex chapter

We pointed users of the TitanIndexRepair class to the API docs for
more information, but TitanIndexRepair is not included in the API docs
because those docs only cover titan-core.  Removing te links from the
chapter for now, but this is just a band-aid; TitanIndexRepair is a
user-facing public interface and should be part of the API docs in the
future.
Reimplement Faunus incremental loading (+ tests)

The config key for the incremental loading groovy script is currently
titan.hadoop.output.loader-script-file.  It should contain one or more
of the following methods:

* getOrCreateVertex(FaunusVertex, TitanGraph, Context, Logger)
* getOrCreateVertexProperty(TitanProperty, TitanVertex,
                            TitanGraph, Context, Logger)
* getOrCreateEdge(FaunusEdge, TitanVertex /* in */,
                  TitanVertex /* out */,
                  TitanGraph, Context, Logger)

The first method should return a TitanVertex and the last should
return a TitanEdge.  The return type of the middle method is currently
ignored.  In practice, the TitanProperty-typed parameter to the middle
method is always of the more specific FaunusProperty subtype, but
making this explicit would require a cast and doesn't seem to lend
additional functionality.  Might revisit this.

All of the above details are subject to change until this becomes part
of a release.
Ignore the temporary "jobs" dir in Faunus modules