Merge branch 'chris' into cli
Update FileDB with stubs for Database interface

- FileDB does not yet support ModelSEED::Database
  however it won't complain now; this is needed
  for ModelSEED::Database::Composite to work.
Merge branch 'chris' into cli
Foo
Add features to Reference, fix getLinkedObject...

- Added new initialization features for Reference
  Reference->new( ref => "string") # still works
  Refernnce->new( type => "model", alias => "chenry/main" )
  Reference->new( type => "model", uuid => ":uuid")
  ... read the POD for details

- fix getLinkedObjects for getting top-level links

- fix serializeToDB bug:
  Bug occured where an un-Moose'd object would
  serialize with the parent reference, causing JSON
  to puke.

- fix bug circular references with un-Moose'd objects:
  $object->{data}->{parent} needs to be weakned.
Fix issue with annotation import

- Bug where an annotation's custom mapping
  was not being saved.
Allow MongoDBSimple to save uuid objects

- save_data("ref", "obj") will work with
  ref pointing to an existing uuid. A
  new uuid is created and ancestor pointers
  are updated.
Fix errors in ModelDriverV2

- errors using om when it should be store
Fix weak_ref bug in top-level object links

- Bug: top level objects have links to other top
  level objects. E.g. mapping has a link to a
  biochemistry. Previously these were weak_refs
  like other links. However, since these are provided
  by ModelSEED::Store and that class doesn not hold
  onto references to objects, this caused these
  links to be garbage collected.

- Added 'weak' => boolean value to Definitions
- If this value is defined and false, ObjectBuilder.pl
  will not add a weak_ref => 1 tag to the attribute
  properties.
Adding support for better references

- Support ancestor_uuids subobjects
- Support for annotations, models subobjects
Merge branch 'chenry_newdb_reconciliation' of github.com:ModelSEED/Model-SEED-core into cli

Conflicts:
	lib/ModelSEED/MS/BaseObject.pm
Fixing biochemistry import
Adding verbose option to PPOFactory

- Add option to print verbose progress on
  biochemistry import.

- Fix bug with reactioninstance aliases.
  Capitalization of ReactionInstance is not correct.
Adding genome command and support in Annotation

- Adding 'genome' command with support for:
    $ genome roles <alias> # list roles in annotation
    $ genome readable <alias> # print readable annotation obj.

- Create ModelSEED::App::Helpers ( helper functions for CLI )
- Add roles, subsystems functions to Annoation.pm
Improving ms defaults
Add import model support, fix mapping import

- Adding support to import model from FBAMODEL (remote SEED)
  This works now, will soon fix PPOFactory import and add
  support for a --location local import of Models.

- Improve documetation and fix mapping import

- Fix bug dealing with annotation object in model import
Initial draft of model command

- Supports readable right now
- Working towards support for SBML (need to fix bugs)
Initial get command, improve list command

- Initial draft of get command: supports only --raw
  flag to output raw JSON (will support readable soon)

- Fix list to support ancestor_uuids, use Helper class
Merge changes from stash
Fix alias functions, builder function names

- Fix alias functions: stop them from printing
  to STDOUT when an alias isn't found. Just return
  undef. Related fix to _build_id function to return
  uuid if getAlias returns undef.

- Fix alias related function: defaultNameSpace,
  this should now work for objects that are more than one
  step below the object containing the aliases.

- Rename builders to be more readable: _build_$attribute