Fix server directory structure input

[a3ng7n]

(includes changes from #259 )

This makes clicking on a file in the directory structure insert the full file path to the include/exclude pattern. It does this by changing the output of _create_tree_structure from a single newline delimited string, to a list of those same lines, in tuples with the corresponding file path they represent.

The api interface that the user sees for ingest_query and format_node is kept the same; they both still output a tuple of three strings. But there's some added lifting to process_query to regenerate the context-aware directory tree, and use that within the html/js interaction functions. To eliminate this regeneration would mean either a very different architecture or changing the interfaces for ingest_query and format_node, both of which didn't seem like the right call.

keeping this as draft until if/when #259 gets merged