Changes all usages of runMongoProgram(<mongo tool>, ...) to
MongoRunner.runMongoTool(<mongo tool>, {...}) to take advantage of the
--dialTimeout command line option supported by the mongo tools.
Adds support for specifying positional arguments to
MongoRunner.runMongoTool() in order to support all invocations of the
bsondump and mongofiles tools.
This is just a cleanup work to hide some of the private state of
ReplSetTest so it is easier to encapsulate and add new logic. Also enables
strict mode.
