refactor InputFormat and InputEntityReader implementations

[clintropolis]

This PR makes a minor refactor to #8823, modifying InputFormat.createReader to supply InputEntity and the temp dir to create the reader instead of supplying it to the read and sample methods of InputEntityReader, since a reader is intended to be tied to a single InputEntity.

[jihoonson]

I think it makes more sense since the interface now says more clearly that InputEntityReader is stateful. +1 after CI.

[clintropolis]

lgtm seems to be having issues running all PRs, the failure doesn't seem specific to this one:

[2019-11-16 00:05:58] [autobuild] [INFO] Running 'npm ci' in /opt/src/web-console
[2019-11-16 00:08:00] [autobuild] [ERROR] npm ERR! code E400
[2019-11-16 00:08:00] [autobuild] [ERROR] npm ERR! 400 Bad Request: domhandler@2.4.2

Going to merge this anyway, since I have two +1s and this is blocking something else I'm trying to work on.