Committing new branch for dynamic moose file capability. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Forgot to drag the Manifest file in the git staging view. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Committing current work to branch regarding yaml file generation from
eclipse toolbar. 
Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Merged latest from Master to this branch (Jordan's bug fixes and Anna's
Discrete Moose paramters work). 

Adding a new Eclipse toolbar button, handler, and wizard for generating
MOOSE yaml and action syntax files, locally or remotely. This is a first
pass, feel free to review and provide feedback. 


Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Merge remote-tracking branch 'origin/master' into dynamic_moose_files

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Merge remote-tracking branch 'origin/master' into dynamic_moose_files

Conflicts:
	src/org.eclipse.ice.item/src/org/eclipse/ice/item/nuclear/MOOSELauncher.java

Merging Anna's bug fix into this branch. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Added a new icon for generate yaml button. Still not great, but better
than the string that was there.

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Committing initial stab at IOService, IReader, and IWriter, as well as
MOOSEFileHandler's implementation of IReader and IWriter methods. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Added some more logic checks to updateFileEntries so it can be less
breaky.

Signed-off-by: Anna Wojtowicz <wojtowicza@ornl.gov>
Committing update for IO services. Item now receives an IOService, and
IOService receives IReaders and IWriters via OSGi Declarative Services.
MOOSEFileHandler now realizes both the IReader and IWriter interface and
provides implementations that enable dynamic file entry generation
depending on the user-selected input file. This is handled at the Item
and JobLauncher level. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Merge remote-tracking branch 'origin/master' into dynamic_moose_files

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Fixing a bug where commented out parameters were being processed by the
MOOSE launcher.

Signed-off-by: Jordan Deyton <deytonjh@ornl.gov>
Merge branch 'dynamic_moose_files' of https://github.com/eclipse/ice into dynamic_moose_files
Fixing a few tests related to the new MOOSE IO infrastructure. Setup
MOOSEFileHandler.findAll to change the name of the File Entry to its
parent Blocks name if the Entry's current name is the general 'file' or
'data_file' to make the Entry more descriptive for the MOOSE user. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Put some logic checks back in.

Signed-off-by: Anna Wojtowicz <wojtowicza@ornl.gov>
Merge branch 'dynamic_moose_files' of https://github.com/eclipse/ice into dynamic_moose_files
Put some logic checks back in.

Signed-off-by: Anna Wojtowicz <wojtowicza@ornl.gov>
Merge remote-tracking branch 'origin/master' into dynamic_moose_files

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Merge remote-tracking branch 'origin/master' into dynamic_moose_files

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>
Committing updates to Item, JobLauncher, JobLaunchAction, and
MooseLauncher. Implemented JobLauncher.getWorkingDirectory() to let
subclasses get a reference to the absolute path of the
iceLaunch_timestamp working directory. 

Removed code in JobLaunchAction.launchLocal that moves generated files
into the default project space. Added code to JobLauncher.launchRemotely
that creates a local remoteIceLaunch_timestamp directory to serve as a
place for downloaded files from the remote host. 

Added file creation/copying/moving functionality to the Item.
Implemented copyFile(s), moveFile(s), getFiles, and deleteDirectory that
subclasses can utilize for simulation file manipulation. 

Reimplemented MOOSELauncher.updateResourceComponent to use these new
Item methods. 

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>