User guide enhancements

This is an overhaul of the user guide.

Overall it does the following:

• Some renames in the section titles
• Split the junctions documentation into multiple sections
  • Initial section demonstrating how to make a simple junction
  • Separate (now enhanced) section on how to use workspaces with junctions
  • New chapter added about using project options and include files in the context of subprojects
• New chapter to the getting started section about project options and directives in general
• New chapter added to the Developing section about using strict mode in conjunction with workspaces
• New section about Handling files
  • New chapter about Compositions
  • New chapter about Filtering
  • New chapter about Overlapping files