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.