refactor: lead provenance, unified link path, SSOT cleanup, configurable weights

Five interrelated cleanups:

1. Lead -> Phenomenon provenance
   - Phenomenon.from_lead_id field on the dataclass
   - BaseAgent.run(lead_id=...) writes self._current_lead_id
   - _add_phenomenon auto-injects from agent state (LLM unaware)
   - Orchestrator dispatch passes lead.id; Phase 1/2-auto/4/5 stay None
   - Merge path preserves the first non-None lead_id on collision

2. Unified Phenomenon <-> Hypothesis link path
   - HypothesisAgent only adds hypotheses, never links
   - link_phenomenon_to_hypothesis tool + executor removed
   - All links go through Orchestrator._judge_new_phenomena
   - Phase 2 unconditionally judges after hypothesis generation
   - Gap Analysis judges after each dispatch round
   (Three previously-missing judge calls now in place.)

3. SSOT in agent subclasses
   - Remove RoleTemplate dataclass, ROLE_TEMPLATES dict,
     _instantiate_from_template method
   - Each agent subclass owns name, role, and tool list
   - agent_factory.py shrinks from 299 to 153 lines
   - All 7 agents now route through _AGENT_CLASSES (filesystem,
     registry, communication, network, timeline were previously dead
     subclasses overridden by templates)

4. Configurable edge weights
   - HYPOTHESIS_EDGE_WEIGHTS -> _DEFAULT_EDGE_WEIGHTS (private default)
   - EvidenceGraph(edge_weights=...) override via config.yaml
   - hypothesis_edge_weights section in config.yaml (commented example)
   - main.py and regenerate_report.py read and pass through

5. regenerate_report.py auto-picks the latest run/*/graph_state.json
   when no CLI arg is given (was a hardcoded date path)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

base_agent.py

@@ -37,6 +37,7 @@ class BaseAgent:
         self._tools: dict[str, dict] = {}  # name -> schema
         self._executors: dict[str, Any] = {}  # name -> async callable
         self._work_log: list[str] = []
+        self._current_lead_id: str | None = None
 
     def register_tool(
         self,
@@ -107,11 +108,12 @@ class BaseAgent:
             f"- Do NOT fabricate execution timestamps — only report timestamps returned by tools"
         )
 
-    async def run(self, task: str) -> str:
+    async def run(self, task: str, lead_id: str | None = None) -> str:
         """Run this agent with a specific task."""
         _log(task, event="agent_start", agent=self.name)
         self.graph.agent_status[self.name] = "running"
         self.graph._current_agent = self.name
+        self._current_lead_id = lead_id
 
         self._register_graph_tools()
 
@@ -375,6 +377,7 @@ class BaseAgent:
             raw_data=raw_data,
             timestamp=timestamp,
             source_tool=source_tool,
+            from_lead_id=self._current_lead_id,
         )
         if merged:
             return f"Phenomenon merged into existing: {pid} — {title} (corroboration boost)"