refactor: hide legacy analysis behind internal surfaces

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-opencode)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

Author: Her-xanadu

scripts/docker/scientific-task-smoke.ts

@@ -6,17 +6,20 @@ import {
   experiment_init,
   experiment_plan_or_resume,
   experiment_prepare_sandbox,
-  experiment_run_analysis,
   experiment_run_governed_workflow,
   experiment_status,
   experiment_validate_spec,
 } from "../../src/tools";
-import { pathExists, readJsonl } from "../../src/utils/fs";
+import { aggregateProposals } from "../../src/analysis/aggregator";
+import { resultPacketSchema } from "../../src/analysis/result-packet";
+import { runTriModelAnalysis } from "../../src/analysis/tri-model";
+import { pathExists, readJson, readJsonl } from "../../src/utils/fs";
 import {
   getCompatGoalPath,
   getBestPath,
   getOrchestrationSummaryPath,
   getOrchestrationTracePath,
+  getResultPacketPath,
   getProposalCardsPath,
   getRunsPath,
   getSessionPath,
@@ -92,7 +95,8 @@ async function main() {
   );
   const planned = JSON.parse(await experiment_plan_or_resume.execute({ workspace_root: workspaceRoot }));
   const workflow = JSON.parse(await experiment_run_governed_workflow.execute({ workspace_root: workspaceRoot }));
-  const analysis = JSON.parse(await experiment_run_analysis.execute({ workspace_root: workspaceRoot }));
+  const packet = resultPacketSchema.parse(await readJson(getResultPacketPath(workspaceRoot), null));
+  const analysis = aggregateProposals(runTriModelAnalysis(packet));
   const status = JSON.parse(await experiment_status.execute({ workspace_root: workspaceRoot }));
   const acceptance = JSON.parse(await experiment_acceptance_review.execute({ workspace_root: workspaceRoot }));
 

src/agents/sisyphus-experiment-orchestrator.ts

@@ -53,7 +53,6 @@ Output contract:
     experiment_decide_iteration: true,
     experiment_status: true,
     experiment_acceptance_review: true,
-    experiment_run_analysis: true,
     experiment_controller_bootstrap: true,
     experiment_controller_start: true,
     experiment_controller_tick: true,

src/tools/index.ts

@@ -200,7 +200,7 @@ export const experiment_acceptance_review: ToolDefinition = tool({
 });
 
 export const experiment_run_analysis: ToolDefinition = tool({
-  description: "Run legacy tri-model placeholder analysis for the current result packet and persist compatibility proposal cards.",
+  description: "Internal/test-only legacy tri-model placeholder analysis for the current result packet.",
   args: {
     workspace_root: tool.schema.string().optional(),
   },
@@ -436,7 +436,6 @@ export function createExperimentTools(runtime?: PluginInput): Record<string, Too
     experiment_decide_iteration,
     experiment_status,
     experiment_acceptance_review,
-    experiment_run_analysis,
     experiment_controller_apply_mutation,
     experiment_controller_bootstrap,
     experiment_controller_start,

tests/e2e/e2e.test.ts

@@ -2,9 +2,12 @@ import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
 import { afterEach, describe, expect, it } from "vitest";
-import { experiment_execute_iteration, experiment_init, experiment_run_analysis, experiment_run_governed_workflow, experiment_status } from "../../src/tools";
-import { readJsonl } from "../../src/utils/fs";
-import { getOrchestrationTracePath, getRecoveryCheckpointPath } from "../../src/utils/paths";
+import { aggregateProposals } from "../../src/analysis/aggregator";
+import { resultPacketSchema } from "../../src/analysis/result-packet";
+import { runTriModelAnalysis } from "../../src/analysis/tri-model";
+import { experiment_execute_iteration, experiment_init, experiment_run_governed_workflow, experiment_status } from "../../src/tools";
+import { readJson, readJsonl } from "../../src/utils/fs";
+import { getOrchestrationTracePath, getRecoveryCheckpointPath, getResultPacketPath } from "../../src/utils/paths";
 
 const tempDirs: string[] = [];
 
@@ -49,7 +52,8 @@ describe("local e2e", () => {
         params: { key: "learning_rate", value: 0.9 },
       },
     });
-    const analysis = JSON.parse(await experiment_run_analysis.execute({ workspace_root: workspace }));
+    const packet = resultPacketSchema.parse(await readJson(getResultPacketPath(workspace), null));
+    const analysis = aggregateProposals(runTriModelAnalysis(packet));
     await fs.mkdir(path.dirname(getRecoveryCheckpointPath(workspace)), { recursive: true });
     await fs.writeFile(
       getRecoveryCheckpointPath(workspace),