Merge pull request #39 from blazetopher/refactor_coverage

Refactor coverage
Modifies method by which bricks are managed.  Initial trial.

Creation seems to be working, loading does not.
Migrates brick metadata to master file.
Adds read_only flag to ParameterManager
Adds sharing of domain objects

Adds _assign_domain function - allows ParameterContexts added to a coverage to share the temporal and spatial domain objects of the coverage, rather than just the extents information.

Also allows _assign_domain to be called during load to ensure ParameterContexts use shared domain objects after reloading a coverage
Isolates creation of virtual bricks from each parameter initialization.

Many log.warn added, must be removed in future commit.
Removes references to parameter_name in the brick_list.
Changes order of MasterManager initialization of the brick_tree.
Updates insert_timesteps to call expand_domain only once.  Fixes method by which external links are added to the master file.

Reverts test_coverage_basics.test_create_multi_bricks to not use a parameter name.
Consolidates logging statements and removes unused commented code.  Fixes test_create_multi_bricks.

Prepares code for rebase with mutli_dim branch.
Fixes coverage constructor bug
Addresses issue when constructing a coverage with an existing temporal domain of shape > 0