feat(refit): complete S1-S6 — case abstraction, grounding, log-odds, plugins, coref, multi-source
Consolidates the long-running refit work (DESIGN.md as authoritative spec)
into a single baseline commit. Six stages landed together:
S1 Case + EvidenceSource abstraction; tools parameterised by source_id
(case.py, main.py multi-source bootstrap, .bin extension support)
S2 Grounding gateway in add_phenomenon: verified_facts cite real
ToolInvocation ids; substring / normalised match enforced; agent +
task scope checked. Phenomenon.description split into verified_facts
(grounded) + interpretation (free text). [invocation: inv-xxx]
prefix on every wrapped tool result so the LLM can cite.
S3 Confidence as additive log-odds: edge_type → log10(LR) calibration
table; commutative updates; supported / refuted thresholds derived
from log_odds; hypothesis × evidence matrix view.
S4 iOS plugin: unzip_archive + parse_plist / sqlite_tables /
sqlite_query / parse_ios_keychain / read_idevice_info;
IOSArtifactAgent; SOURCE_TYPE_AGENTS routing.
S5 Cross-source entity resolution: typed identifiers on Entity,
observe_identity gateway, auto coref hypothesis with shared /
conflicting strong/weak LR edges, reversible same_as edges,
actor_clusters() view.
S6 Android partition probe + AndroidArtifactAgent; MediaAgent with
OCR fallback; orchestrator Phase 1 iterates every analysable
source; platform-aware get_triage_agent_type; ReportAgent renders
actor clusters + per-source breakdown.
142 unit tests / 1 skipped — full coverage of the new gateway, log-odds
math, coref hypothesis fall-out, and orchestrator multi-source dispatch.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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