#155 Linearization preserves more model structure and absolute names.

Linearization preserves more of the original model structure and absolute names + other changes:

• CifCollectUtils: added collectDeclarations/collectIoDeclarations.
• LinearizationBase
  • No longer eliminates groups (and thus no longer pushes I/O file declarations inwards).
  • Replaces original automata by groups.
  • Now only moves disc/cont var declarations to new automaton.
    • Variable names in new aut based on original absolute names.
  • No longer moves inits/marked/invs from components to the new aut.
    • Inits/markeds/invs from locs still merged to new aut.
  • No longer merges I/O declarations into the new automaton.
  • No longer merges all enumerations to a single enumeration (and thus no longer adds default initial values).
  • removeChannelDataTypes: much simpler code now.
  • handleUrgency: does not actually need the specification.
  • Linearization may now produce models with scope absolute reference.
• LinearizeMerge
  • Use absolute event names now for warning messages.
• Various JavaDoc and comment improvements.
• CifToPlcTrans
  • Updated CIF PLC code generator for linearization changes.
  • Still merges enums.
  • Now collects declarations from all components.
  • Improved absolute names in error messages, generated comments, etc.
  • Generated PLC code has some backward incompatible name changes.
    • Global variables have less 'M' of linearized automaton in names.
• CodeGen
  • CIF code generator updated for linearization changes.
  • Still pushes print file declarations into print declarations.
  • Still merges enums.
  • Now collects declarations from all components.
  • Improved original event absolute names.
  • Improved absolute names in generated comments.
  • Improved print declaration order.
• Linearization test updates.
  • Realigned linearization product/merge test models.
  • Removed linearization enum merge test as enums no longer merged.
  • Linearization tests for renames updated for recent changes.
• Linearization documentation updates and improvements.
• CIF PLC code generator tests and documentation updated.
• CIF code generator tests and documentation updated.

Closes #155 (closed)