Pass through all files to collect data before generating documentation

[kiith-sa]

Collect all functions, classes and other items (reuse/modify visitor.Item), together with their source locations, fully qualified names, how many times each item is referenced, etc. (Keep the AST node of each item as well; the overhead should be manageable).

Needed for many other issues, e.g. cross-referencing, class list sidebar, default main page, semantic highlighting, etc.

This pass can be merged with the existing pass that collects links for the TOC.

[kiith-sa]

As of 832c901 much of this is done (but will need more work to start fixing some of the depending issues)