GNN v3.5.0 — Surface Truth & Integration

GNN v3.5.0 — Surface Truth & Integration

This release makes the package's outward surfaces honest and connected. The
website dashboard reads step statuses from the recorded pipeline execution
summary instead of guessing from directories; MCP clients speak the standard
2024-11-05 protocol in both transports, with three new tools (extract_pomdp,
generate_dependency_graph, template.pull) and a gnn_delete_run parity
tool. DELETE /api/v1/runs/{run_hash} now gives the API full run control —
proper cancellation with process-group teardown, artifact removal, and honest
status on timeout. The GUI estate got a truth pass: launches are verified over
HTTP instead of assumed, status artifacts share one schema, gui_1/gui_2/gui_3
and oxdraw gained dozens of UX and round-trip fidelity fixes, and a new
gnn gui subcommand puts the interactive stack on the CLI. Under the hood,
one canonical framework tuple drives every framework list (fixing the
--frameworks stan abort and silent lean filtering), step 24 gains
content-addressed LLM response caching, LSP diagnostics track in-editor
edits, and visualization imports got ~30% faster by making seaborn/scipy load
lazily.

Release stabilization (2026-09-22): after the initial tag, the CI matrix
surfaced a chain of green-gate fixes that are part of this release: the
version-literal reconciliation (gnn.__version__, api.MODULE_VERSION,
version-consistency tests), cross_framework runtime threading beside the new
timeout parameter, a flax marker-gate (flax 0.12.9 for the jax-0.11.2
py3.12 splits — 0.12.6 calls a jax API removed in 0.11.0), the mypy target
moved to 3.12 (numpy 2.4.x stubs), the executor lazy-loader reconciliation
carrying the ngclearn spec row, and a seaborn center= fix that routed the
correlation heatmap through a warning-raised Colormap.set_bad(). The tag
now points at the fully green tip.