Update mate2

[julesghub]

Changes for M@TE2.

Now model repos will do the update_doi.py step slightly differently.
No longer is the .website_material/ directory used or updated.

A description of the changes made.

file_utils.py — create_or_update_json_entry now:

• resolves entities by full @id or its last path segment (so model_code_inputs matches http://example.org/base/model_code_inputs)
• matches the root token ./ to the root Dataset (id ./ or a Dataset whose id ends in /)
• raises KeyError instead of silently print+return, so failures are explicit

parse_utils.py:

• new _find_root_entity() used by both format_citation and ro_crate_to_cff (handles the http://example.org/base/ root, not just ./)
• guarded ro_crate_to_cff against empty identifier → no more IndexError mid-script

update_doi.py:

• retargeted the model entity writes to the real model_code_inputs / model_output_data, as best-effort (warning, not fatal, if absent)
• root identifier + creditText writes now actually land