merge
=====
Restarting a FLASH run with flmake generates a new run directory and id.  This is because 
for FLASH to restart the runtime parameter file (``flash.par``) must be changed.  After 
many (or even one) restart it is sometimes useful to have all of the data from a run history
to be collapsed into a single directory.  The ``flmake merge`` command does exactly this
in a way that is `atomic`_ with all runs.  Therefore merges

* act on the latest run in history that the user wishes to merge
* generate a new, independent run id and directory
* copy - rather than symbolically link - all data.

Moreover runtime files, such as ``flash.par`` and ``flash_desc.json``, from previous runs
in history are renamed in the merge using the following convention: ``flash.{runid}.par``.

**USAGE**:: 

    flmake merge <leaf-dir|id> [<target-dir>]

Either the directory or the run id of the latest restart must be specified in order 
to merge.  Optionally, a target directory to place the merge in may also be given.  If
omitted then the default run directory name is used.

.. _atomic: http://en.wikipedia.org/wiki/Atomicity_(database_systems)