Add causal-edge mode to deep-research-community (Edison, one community)

[realmarcin]

What

Extends the Edison deep-research-community skill with a causal-edge mode:
for a single community, it asks Edison (PaperQA3) to build a source-backed causal
interaction graph — interaction nodes (type, scope, source→target taxa,
metabolites/processes, +/− sign) and directed causal edges ("A enables/drives/
suppresses B").

Maps straight onto the schema:

• nodes → ecological_interactions[] (interaction_type, scope, source_taxon→
  target_taxon, metabolites, biological_processes)
• edges → EcologicalInteraction.downstream[] (InteractionDownstream: target +
  causal-link description)

Changes

• templates/community_causal_graph_research.md — new causal template. Reuses
  the same placeholders as the mechanism template, so the existing
  render_query / template_vars machinery is unchanged. Requires a verbatim
  snippet + CURIEs per node and per edge; asks for a node table, an edge table,
  and a DOT/adjacency sketch; flags hypothesized vs demonstrated edges.
• scripts/research_community_edison.py — add --label to suffix output
  filenames, so a causal run (--label causal) does not overwrite the default
  mechanism run for the same community+job. Label is recorded in the meta yaml.
• justfile — just research-community-causal <target> (causal template +
  --label causal), same Edison plumbing/provenance as research-community-edison.
• skill.md — documents the mode: when to use it, output naming, schema mapping,
  and the unchanged curator hand-off (never mutate kb/communities/).

Verified

• Causal template renders against a real community (10360 chars, all placeholders
  resolve).
• just research-community-causal <stem> --dry-run writes
  <stem>-edison-literature-causal(-meta).* — doesn't touch the mechanism run,
  spends no credits.
• Reuses the vendored _edison_capture provenance bundle; scoped to one
  community at a time (as requested).

Scope note: research/report only — like the base skill, it does not write to
kb/communities/; a curator applies the reviewed ecological_interactions block.

🤖 Generated with Claude Code

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