fix: rebuild context graph for v3

[benslockedin]

Summary

• Index script (generate-index.py) was v2 — looking for _core/ instead of _kernel/, reading now.json as markdown, scanning for _capsules/ instead of bundles. Every user got broken graph output with 0 bundles detected and ghost _kernel nodes.
• Graph script (generate-graph.py) used circle packing, which is wrong for a network with hierarchy. Replaced with force-directed + domain cluster gravity, based on Obsidian graph view research.

What changed

Index fixes

• Recognize _kernel/ as walnut parent dir (v3 structure)
• Read now.json as JSON (was parsing as markdown frontmatter)
• Detect bundles via context.manifest.yaml (was scanning _capsules/)
• Infer parent-child from filesystem hierarchy (nested walnuts auto-link)
• Bidirectional people-walnut links (person walnut links: → walnut people:)
• Strip [[wikilinks]] on read — handles YAML parse issue at consumer level
• Enrich with now.json: task counts, bundle summaries, blockers, session data

Graph rebuild

• Force-directed with domain cluster gravity (Life/Ventures/Experiments/People/Archive)
• Health indicators (green/amber/red border based on rhythm vs last update)
• Detail panel on click (goal, next action, tasks, bundles, people, connections)
• Neighborhood highlighting on hover (dim everything else)
• Task urgency dots + blocker flags directly on nodes
• Semantic zoom, search, dark mode, people toggle, archive toggle

Test plan

• Run python3 .alive/scripts/generate-index.py — verify walnuts detected, bundles > 0
• Run python3 .alive/scripts/generate-graph.py — verify HTML generated
• Open graph — verify domain clusters, click nodes for detail panel
• Test with v2 world (has _core/, _capsules/) — verify backward compat
• Test [[wikilink]] in linked_bundles: field — verify no YAML parse error
• Test on Windows with py -3 fallback

🤖 Generated with Claude Code

[patrickSupernormal]

Merge safety review (advisory) — Patrick Brosnan, non-collaborator on alivecontext/alive. Comment weight only, not an approving review.

Verdict: YELLOW — R-1 silent regression, must fix before merge. Blocked on PR #29 landing.

Headline: The visual redesign is a strict improvement — the Obsidian-style force-directed graph with domain gravity wells, neighborhood highlighting, semantic zoom, and the click-to-pin detail panel all read cleanly. Health-ring computation matches plugins/alive/rules/world.md exactly. No bugs in the graph script itself. But the generate-index.py rewrite has one silent behavioural regression and several smaller cleanup items.

R-1 (CRITICAL): top-level recent_sessions: and unsigned_with_stash: removed from _index.yaml and _index.json.

The OLD code computed a world-level recent_sessions list by walking .alive/_squirrels/*.yaml (mtime-sorted, top 10) plus an unsigned_with_stash counter. The NEW code deletes both and replaces them with a PER-WALNUT session_count and last_session derived from that walnut's own now.json.recent_sessions — useful enrichment, but it lives on individual walnut entries, not at the top level.

Verified downstream breakage via GitHub code search on alivecontext/alive@main: plugins/alive/skills/world/SKILL.md (SHA e6e14b9) lines 21, 67, 198 explicitly document "Unsigned squirrels with stash: already in the index as unsigned_with_stash:" and "recent sessions are in the index under recent_sessions: and unsigned stash count is in unsigned_with_stash:. DO NOT read .alive/_squirrels/.yaml files"*. After #31 merges, those two fields will be absent. The /alive:world dashboard — the most-invoked skill in the system — either silently renders without the session pulse / attention section, or crashes on a missing-field read.

Fix path: Restore both computations verbatim in generate-index.py before the YAML/JSON write (the old code in the diff is the correct implementation — removal looks accidental, the PR body doesn't mention it). Keep the new per-walnut enrichment. Both can coexist — they answer different questions.

Also worth fixing:

• R-2: Graph loses the "world root" centrepiece node and the "inputs" buffer node. Either restore as pinned-centre "special: true" nodes, OR update docs/skills to no longer reference them.
• R-3 to R-7: Stats header drops inputs/sessions; display label "bundles" vs underlying key capsules mismatch; dead 3-nested-loop code in bidirectional-links; exception handler in now.json reader breaks out of the candidate loop on JSONDecodeError (stopping fall-through to v2 path); module docstring downgraded from "v3" back to "v2" (looks like a merge accident).

Merge order: Position 5 of 5 (last), immediately after #29. Base SHA de8d602 verified identical to PR #29 HEAD SHA — #31 has fully absorbed #29's tip, zero textual conflict on either file, but GitHub won't let #31 merge to main before #29 because baseRefName: v3-projection-redesign only exists on the #29 side. Cannot merge before #29.

Before merging, run python3 .alive/scripts/generate-index.py locally and grep -c 'recent_sessions\|unsigned_with_stash' .alive/_index.yaml — if the count is zero, R-1 is unfixed.

Full cross-PR synthesis (conflict matrix, recommended merge order for all 7 open PRs, per-PR verdicts, blocker list): see the cover comment on #29 — #29 (comment)

Generated via flow-next epic fn-8-vly (stackwalnuts walnut). 🐿️