A hyperedge's member list is canonically keyed `nodes`, but producers
(LLM/subagent drift, externally-supplied graph.json) sometimes emit
`members` or `node_ids` — graphify only read `nodes`, so those hyperedges
silently lost their members, and semantic_cleanup's prune dropped them
entirely. Normalize the member key to `nodes` at one ingest chokepoint in
build_from_json (and in semantic_cleanup, which runs pre-build), deduping
and warning, so every downstream consumer sees the canonical key. Mirrors
the existing from/to edge-endpoint aliasing.
Reported by @askalot-io.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1418: build_from_json relativized source_file on nodes and edges but stored
graph.hyperedges[] verbatim, so a semantic subagent's absolute path leaked into
graph.json. Relativize hyperedges in build_from_json (to_json has no root to
relativize against), mirroring the existing node/edge handling.
#1423: consolidate the GRAPHIFY_OUT output-dir name into a single graphify.paths
module (was duplicated in __main__, cache, watch) and route the path guards
through it — security.validate_graph_path's base=None discovery + fallback,
callflow_html's project-root resolution, and the post-commit/post-checkout hook
bodies (which now read the env var at hook-run time). A renamed output dir is no
longer validated against the wrong base or missed by the hook.
Tests: hyperedge relativization (test_hypergraph), GRAPHIFY_OUT discovery
(test_security), updated the hook-body contract assertion (test_hooks).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
safishamsi