Refresh Usage Principles landing-page diagrams: swap in the new data-flow infogram + drop the mini-ecosystem figure

[breimanntools]

Problem

The Usage Principles landing page (docs/source/index/usage_principles.rst) carries two figures that are now stale or redundant:

• connections.png (figure at usage_principles.rst:32, "General pipeline for sequence-based protein prediction") is effectively a small, older version of the new AAanalysis ecosystem map (docs/source/_static/aaanalysis_ecosystem.html). Having both means two competing "where AAanalysis fits / what feeds it" graphics that can drift apart and confuse readers.
• components.png (figure at usage_principles.rst:49, the df_seq → df_parts → df_feat data-flow diagram) predates the current API vocabulary and is slated to be replaced by a new, cleaner data-flow infogram.

Until refreshed, the first scroll of the page — whose whole job is to teach the canonical workflow — mixes an outdated pipeline graphic with a redundant mini-ecosystem.

Goal

Refresh the Usage Principles page so it shows exactly one current data-flow infogram and no longer duplicates the ecosystem map — consuming the new data-flow infogram asset once it exists.

Requirements

• Replace the components.png figure (usage_principles.rst:49) with the new data-flow infogram asset: drop it into _artwork/diagrams/, update the .. figure:: path and caption to the current vocabulary (df_seq, df_parts, split_kws, df_feat; SequenceFeature / CPP / AAclust / dPULearn).
• Remove or replace the connections.png figure (usage_principles.rst:32): either delete it and point readers to the ecosystem map (_static/aaanalysis_ecosystem.html) in prose, or replace it with a trimmed view that is clearly not a duplicate of the full map. Decide remove-vs-replace during implementation.
• Reconcile the surrounding prose (usage_principles.rst:23-45) with whatever figures remain — no dangling references to a removed figure, captions match the new assets.
• Keep the README consistent if either figure is reused there.

KPIs / Acceptance criteria

• cd docs && make html builds with no new warnings and no broken image/figure references on the Usage Principles page.
• Exactly one data-flow diagram remains on the page, using the new infogram; zero references to the old components.png.
• The connections.png mini-ecosystem is either gone (with a prose link to the ecosystem map) or visibly distinct from it — no two near-duplicate ecosystem graphics remain in the docs.
• Page renders correctly on RTD latest after merge (visual check).

Scope / non-goals

• Out of scope: authoring the new data-flow infogram artwork itself — that is the upstream task this issue consumes (see Dependencies).
• Docs / artwork only; no library code changes.
• Deleting connections.png / components.png from _artwork/diagrams/ is a file deletion → CONFIRM-FIRST (needs explicit permission); call it out in the PR rather than removing silently.

Dependencies

• blocked-by Create the new AAanalysis data-flow infogram (df_seq → df_parts → df_feat → model → explain) #227 — the new data-flow infogram asset must be created first ("we do this after the new data-flow infogram").
• relates epic: ecosystem integration — consume upstream + descriptors, expose downstream (sklearn / XAI / design) #210 (ecosystem-integration epic) — the ecosystem map that connections.png redundantly duplicates.

Standards checklist

• Docs-only; no frontend/backend or CONFIRM-FIRST code surfaces touched.
• Any _artwork/ image deletion flagged for permission in the PR.
• README ↔ RTD figure parity checked.