Change makeflow test TR_makeflow_remote_naming to check for both successful translation of filenames and for avoidance of cache conflicts.
Modify work_queue to create "cache" and "uncache" subdirectories to handle cacheable and uncacheable files.
Required adding "flags" entry to multiple work_queue protocol commands.
API is unchanged
Merge branch 'master' of github.com:cooperative-computing-lab/cctools
Fix remote_name test to work correctly on Darwin
More robust commit to fix issues with CONVERT and Darwin
Fixes bug when redifining a variable in makeflow.

Make evident previous memory leak when variables where not boxed.
See also: 5b5df326e19fee6fa491711cbaff4ad5f49ea530
Makeflow gc automatic preserve and collect list

Changes to the garbage collection code:

- reference counts are kept now in the dag (struct dag_file), and
  computed as the dag is constructed/executed, independently of whether
  we are doing gc.

- d->collect_table was changed from a struct hash_table to a struct set.

- incr_file mode was renamed ref_count. Original ref_count and incr_time
  mode were eliminated. on_demand mode left unchanged.

- Variable _MAKEFLOW_COLLECT_LIST was renamed GC_COLLECT_LIST.

- Variable GC_PRESERVE_LIST was added.

- Files to be collected are computed as follows:

((((all_files - sink_files) + GC_COLLECT_LIST) - GC_PRESERVE_LIST) -
source_files)

In which sink_files are targets that are not an input file of some node,
and source_files are the files that are not the target of some node.

In summary:

- If both GC_*_LIST are empty, but nevertheless gc is activated, then
  the files collected are:

  intermediate_files = all_files - sink_files - source_files.

- GC_PRESERVE_LIST takes precedence over GC_COLLECT_LIST.

- sink_files are not collected unless they appear on GC_COLLECT_LIST.

- intermediate files are collected unless they appear on
  GC_PRESERVE_LIST.

- source_files are never collected, even if they appear on
  GC_COLLECT_LIST.
Changes reference counts after recovering log.

Fixes issue 164, in which makeflow would not collect files when
re-running the workflow with gc.
Enable workqueue-sharedfs in Makeflow.

Monitor wrapping does not seem to work, but I was able to run shrimp on
pscratch using absolute paths.
Makeflow uses absolute paths when -Twq_sharedfs

This does not work when a directory needs to be created (e.g., with the
monitor).
do_thirdput creates directory if needed

Patch per Mike suggestion.
Merge pull request #166 from btovar/wq_sharedfs

Enable workqueue-sharedfs in Makeflow.
I added two header files("dttools/src/buffer.h" and "dttools/src/md5.h") into the "PUBLIC_HEADERS"of the "dttools/src/Makefile" file. In this way, the "HOWTO: Write Code that Uses Chirp" on our website will be executed well.
Revert "Modify work_queue to create "cache" and "uncache" subdirectories to handle cacheable and uncacheable files."

This caused us to break both forwards and backwards compatibility, and we figured out a better way to achieve the same goal

This reverts commit f90b39f1a088125b6c1ea41d3dbbb42b40752dfc.

Conflicts:
	work_queue/src/work_queue_worker.c
Alternative fix for name colisions between cached and uncached files.
Less protocol-breaking than f90b39f1a08.

This adds ".cached" to the end of each cached file when stored in the cache directory.
It effectively creates a separate namespace for files declared as cacheable that cannot
be impinged upon by uncached files, and vice-versa.
Adds symlink alternative to link_file_in_workspace().
If "link()" fails due to a permissions or cross-device error, we will now try to symlink the file instead.
This is a partial fix for issue #140
Check for duplicate remote filenames across both input and output files.
If duplicates are specified, throws an error and prints an error message explaining the problem.

Final fix to issue #140
Band-aid for issue #64.

This prevents a task from clogging the queue, but doesn't address what we should do if a task cannot be run by any worker, and doesn't intelligently schedule tasks that are resource hogs.
Added printf attribute to buffer_printf, and fixed corresponding type mismatches.
Added printf attribute to link_putfstring, and fixed corresponding type mismatches.