Add support to index entire projects instead of file-by-file basis

[rsdunlapiv]

Optimization for real codes; scaling to large number of files; directory hierarchy

[rsdunlapiv]

This would be necessary for any code generation that requires changing multiple source files. One example would be adding a mediator to a NUOPC application while looking at the driver code. It would also open the door to supporting major code generation scenarios, e.g., "two component system w/ explicit coupling" and the like.