Adding commands to support import of SBML files
Start of model-build refactor
Clean up ModelSEED::utilities to be less garish

- ARGS is now args, with modified syntax.
- VERBOSEMSG is now verbose, with modified syntax.
- SETVERBOSE is now set_verbose, with modified syntax.
- Update codebase to reflect these changes.

See POD document for details on the syntax changes.
Add tests
Created mergebio command as placeholder.
Merge pull request #120 from ModelSEED/refactor-utils

Clean up ModelSEED::utilities to be less garish
Merge pull request #118 from ModelSEED/refactor

Start of model-build refactor
Merge branch 'Compound_Reaction_Loading'

Conflicts:
	lib/ModelSEED/MS/Biochemistry.pm
Merge branch 'master' into mergebio
Adding two functions to Reaction.pm and Biochemistry.pm for finding duplicate compounds and reactions
Fixed a bug introduced from prior merge and tested functions on KEGG
Initial draft of bash-completion

- script generateBashCompletionRules that generates
  rules for bash completion. These are put into the
  module:

- ModelSEED::Bash::Completion::Rules, a module with
  rules for doing bash completion. This is read in
  by the bash completion plugin:

- Bash::Completion::Plugins::ModelSEED, a plugin
  that is initialized by the Bash::Completion stuff.

To use, add `source setup-bash-complete` to your
.bashrc or .bash_profile...

TODO :

- implement options that consume args, e.g. --with foo
- implement completion for arguments, e.g. ms list <TAB>
- more unit tests, figure out how to do this properly
Add source setup-bash-completion to bin/dev-env.sh

- Now get bash completion when you normally source
  the development enviornment.
Draft to support bash completion of references

- Now does completion of references that are found
  with `ms list biochemistry/` and other similar
  calls.

- Makes use of a new cache file "~/.modelseed_bash_completion_cache"
  which currently stays valid for 60 seconds. No active cache
  invalidation is done on this yet.

- Add new function to `ms list` command "arg_spec" which just
  defines a set of completion rules for arguments. Real documentation
  on this will be coming soon...

- Currently hitting tab on a "ready-to-complete" string will not
  insert the typical space afterwards. This was done to quickly support
  doing:

    ms list biochemis<TAB>
    ms list biochemistry/<TAB>
    ms list biochemistry/sdevoid/main

  But for cases where we **want** a space inserted, we need to handle
  that now...

TODO:

- improve ms list performance,
- get rid of or become happy with the file cache machanism
- implement "arg_spec" for functions where apropriate
- fix space issue
- mabye implement short "opt_spec" options, match with "-"...
- maybe offer "--" as a completion option to expose flags...
Clean up generateBashCompletionRules function

- Now actually prints out a file if you supply the path
- Has documentation, produces a file with POD!
Better comments for bash-completion driver
Updating usage of ModeSEED::utilities functions, debugged checkForDuplicate functions
Completing mergbio command, and adding code for biochemistry
Merge branch 'mergebio' of https://github.com/ModelSEED/ModelSEED into mergebio

Conflicts:
	lib/ModelSEED/MS/Biochemistry.pm
Completing biomass merge function.