Add explicit call to afterPropertiesSet to a Flow when using Java config

When using java config, the call to SimpleFlow#afterPropertiesSet is not
called in all cases as noted in BATCH-2291.  This commit updates the
builder to explicitly make the call, and updates the SimpleFlow to be
idempotent for calls to afterPropertiesSet.
Fixes the RepositoryItemReader ignoring explicitly set currentItemCount

If the user explicitly sets the currentItemCount value on a
RepositoryItemReader, prior to this commit, it is ignored.  this commit
addresses this by moving the current counter up to the correct value
when that value is set.  This fix addresses BATCH-2274.

This commit also addresses a number of compiler warnings around javadoc.
Updated sequence initalization insert to be idempotent

BATCH-2159 provides a tweak to the insert statement used for
initializing the sequence tables used in the job repository database so
that they don't error if run multiple times as well as don't insert
multiple rows.
BATCH-2242: Stopping a job in STARTING state throws OptimisticLockingFailureException
BATCH-2248: Fixes for Ldif reader tests
Change prefetch on jms tests to 0 and add @DirtiesContext to tests

With the upgrade to ActiveMQ 5.9.0 as part of Spring IO, ActiveMQ's
prefetch behavior changed.  With each call to
JmsTemplate#receiveAndConvert, the template creates a new consumer.  In
these tests, the first call created a consumer which prefetched all the
test messages on the queue, leaving them unavailable for the second
consumer the JmsTemplate created.  By setting prefetch to 0, the
messages are now available for the subsequent
JmsTemplate#receiveAndConvert calls.  This addresses BATCH-2248.
Committing a fix for the loss of offset increments when skippable exceptions are encountered.