Merge pull request #321 from phyloref/improve-documentation

- Added note that definition should include qualifiers (closes #168)
- Documented the CSV export format (related to #257, but I won't close that until I like to it from somewhere in the interface) as [a Markdown file](https://github.com/phyloref/klados/blob/bfae34e42e954920191e3e473f31ee2ae49ffdde/docs/ExportFormats.md).
- Fixed a bug in which we were providing all the expected resolutions before all the actual resolution in the CSV file, despite the header saying that they should be interleaved (i.e. `expected 1, actual 1, expected 2, actual 2`).
- The Open Tree of Life lookup code was previously recording the provenance of the phylogeny in the phylogeny description field, but since this field is no longer used, I've moved it into the phylogeny curator notes field (see example below).
- I accidentally turned on "reformat file on save", and so my IDE changed a bunch of file formatting without me noticing. That shouldn't change any functionality and should be easier to read/maintain in the future, but it's still annoying. 

This PR also closes #300 by modifying the summary table to make it clear that the final columns refer to phylogenies and replacing phylogeny descriptions (which are no longer displayed in Klados) with phylogeny curator notes.

docs/ExportFormats.md

@@ -0,0 +1,30 @@
+# Export Formats
+
+## Summary table CSV export
+
+The summary table CSV export includes the following columns:
+
+* `Phyloreference ID`: A URI (absolute, relative or local; may or may not resolve) that identifies this phyloreference. Normally intended for machine consumption.
+  * Example `#Alligatoridae`
+* `Label`: A label for this phyloreference, normally intended for human consumption.
+  * Example: `Alligatoridae`
+* `Type`: The type of this phyloreference.
+  * May be one of the following values:
+    * `Apomorphy-based clade definition`
+    * `Maximum clade definition`
+    * `Minimum clade definition`
+    * `Invalid definition (...)` (with the reason for the invalid definition in parentheses)
+* `Definition`: The (human readable) clade definition as entered in the `Definition in free-form text`.
+  * Example: `Last common ancestor of Crocodylus niloticus, Osteolaemus tetraspis, and Tomistoma schlegelii and all of its descendents.`
+* `Internal specifier N`: A description of each internal specifier (_N_ is a number starting from 1).
+  * Example: `Caiman crocodilus`
+* `External specifier N`: A description of each external specifier (_N_ is a number starting from 1).
+  * Example: `Caiman crocodilus`
+* `Phylogeny: [Phylogeny label] expected`: The label of the node in the specified phylogeny to which the phyloreference was expected to resolve.
+  * Example: `Alligatoridae`
+  * Will be set to `(none)` if no expected node was found.
+* `Phylogeny: [Phylogeny label] actual`: The label of the node actually resolved for this phyloreference in the specified phylogeny.
+  * Example: `Alligatoridae_ott195670`
+  * Will be set to `(resolution not yet run)` if resolution has not yet been run.
+  * Will be set to `(could not resolve)` if this phyloreference could not be resolved.
+  * Will be set to `(unlabelled)` if a node was resolved, but it had no label.