docs: add tree to file list

[j23414]

Minor edit to the pathogen.json file so that Nextclade Web can find the "tree.json" file. The Nextclade CLI call still works as expected.

Since the final augur tree might not be called "tree.json" could also add instructions to the user to modify the file name.

[j23414]

Still under discussion for where to place this or overall path for the Nextclade dataset docs. From slack:

We were hoping that making most files optional will make it easier for authors - you could start small and then add files gradually, improving the dataset. But now I see it also makes it a bit trickier to understand.

possibility	benefit
only ref	enables only alignment, nucleotide mutation calling, sequencing QC
ref + genome annotation	adds gene level mutations and detail (translation and aa mutational calling)
ref + genome annotation + tree	adds clades classification and phylogenetic placement
ref + tree	uncertain use, perhaps only calling clades and tree placement