Removing transactions from Import
Updating Import to be able to use MySQL

- Import can now write to MySQL database.
- Changes to ModelDB to get it working with
  MySQL ( move linker-table beneath one of it's
  linked tables ).

Conflicts:

	lib/ModelSEED/Import.pm
Changes to CoreApi

- CoreApi now supports a "dsn" initialization option.
  Pass in a standard DBI configuration dsn like:
  "dbi:SQLite:path/to/filename.db" and it will connect.

- Removed the requirement that getBiochemistry, getModel
  have user passed as a parameter.
Getting xml printing of data working

- getPriceData now works. call it like
  a script to get usage information.

- Changes made to CoreApi, Model, Biochemistry,
  Biomass, Reaction, Annotation to better reflect
  the database schema with respect to naming conventions.
Remove readme file
Merge branch 'master' of git://github.com/ModelSEED/Model-SEED-core
Adding a public option for importmodel, particularly useful when re-importing
d
Merge branch 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git

* 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git:
  Adding a public option for importmodel, particularly useful when re-importing
  Remove readme file
  Getting xml printing of data working
  Changes to CoreApi
  Updating Import to be able to use MySQL
  Removing transactions from Import
  Initial revision of generatePriceData
  Removing user as required argument to getModel
  Fixing two bugs, somehow searchnames were not being updated and the stoichiometry of balanced reactants was incorrect
  Fixed return string bug in mdl-changedrains, works fine
  fix bug in FIGMODELreaction::balanceReaction
  Fixed balancing of reactions across multiple compartments.  Currently, if a proton has to be added to a transport reaction, its added to the cytoplasm by default, should be revised
  updated thermodyanmics code and allowing for transporter balancing
  removing mandatory argument from import_model_file
  Fixed erroneous return strings
  Updating cross-checking of MetaCyc and KEGG IDs
  Expanding code to incorporate thermodynamics checking.  Transporters still not balanced and ABC heurstic still not coded, to be done
Printing descriptive output of import model process to file
Fixing bug in ms-workspace
Fixed ProcessMolfiles bug
Fixed bug returning all structural cues for a mol file
Fixed possibly the last bug in the processmolfile function
Adding prefix option to allow different output files to be printed
Automatically generating moose objects, and enabling standardized construction of moose objects from the database.
Merge branch 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git

* 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git:
  Adding prefix option to allow different output files to be printed
  Fixed possibly the last bug in the processmolfile function
  Fixed bug returning all structural cues for a mol file
  Fixed ProcessMolfiles bug
  Fixing bug in ms-workspace
  Printing descriptive output of import model process to file
Work on new File Database. Most of these new features are in FileIndex.pm.
Adjustments introducing uuid type and using meta attributes
Merge branch 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git

* 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git:
  Work on new File Database. Most of these new features are in FileIndex.pm.