Expose lower-level parsing API.

The new functions cmark_new_doc_parser,
cmark_free_doc_parser, cmark_process_line, and cmark_finish
allow you to feed lines one by one (possibly from several
files) to the parser and call finish when you're done.

This is now used in main for mulitple files.
Updated man page for multiple file inputs.
Fixed install target in src/CMakeLists.

Use proper include directory, include needed headers
chunk.h and references.h.