Update wq_submit_workers.common to correctly output help messages with -h or --help.
initialize variables
length of array instead of sizeof(char *)

Reduce number of calls to full_fread by using the whole buffer.
Merge pull request #262 from rampantmonkey/warning_cleanup

Warning cleanup
Catch errors on flush.
Reorganize headers and remove extraneous.
Remove excess redirection in alloc.

Only use chirp_alloc.c when doing an operation that makes an allocation.
Use CFS to get file locks.
Remove unnecessary headers.
Coalesce static variables.
Remove old function declarations.
Move initialization to init.
Rearch of chirp_alloc interface.

o All allocations funneled through single entry chirp_alloc_realloc.
  Commentary: This type of interface limits coupling of modules
  and makes chirp_alloc work similarly to chirp_acl in terms of
  usage.
o Some functions still remain in chirp_alloc but should/could be
  pulled out with some effort:
    * chirp_alloc_[f]stat: Gives a result based on the amount of
      space remaining.
o getstream, putstream, and rmall moved into chirp_server.c:
    * The functionality of getstream/putstream is specialized and
      more appropriately scoped in chirp_server.c.
    * rmall should be reimplemented to always use cfs->rmall. There
      should be a chirp_alloc function which returns the size
      of a directory sub-hierarchy so it can do simple calls
      to chirp_alloc_realloc.
Tests for thirdput and alloc.
Use lowercase SI prefix for Darwin compatibility.
Fix chirp_alloc to use CFS and simplify.

This pull request cleans up chirp_alloc:

o It now uses the CFS layer for access to the file system.
o A lock method was added to the CFS layer. Only local implements it.
o chirp_server now has the implementations of getstream/putstream/rmall since they do not really belong in another module (chirp_alloc).
o chirp_alloc now has a simpler interface like chirp_acl, most requests are funneled through chirp_alloc_realloc.
o 2 new test cases which weakly cover thirdput and alloc.

Fixes #244.
Wrong logic to check if alloc is enabled.
verbose mode to output runtime status of makeflow.

Useful for large workflows which may cause Makeflow to appear unresponsive.
Allow comments inside a rule
Move group variable definitions to header file.