flue refactor and migrations

.npmrc

@@ -0,0 +1 @@
+verify-deps-before-run=false

package.json

@@ -1,53 +1,6 @@
 {
   "name": "code",
   "private": true,
-  "workspaces": {
-    "packages": [
-      "apps/web",
-      "packages/agents",
-      "packages/auth",
-      "packages/backend",
-      "packages/config",
-      "packages/env",
-      "packages/primitives",
-      "packages/ui"
-    ],
-    "catalog": {
-      "@rivet-dev/agentos": "^0.2.7",
-      "@rivet-dev/agentos-core": "^0.2.10",
-      "@effect/platform-bun": "4.0.0-beta.99",
-      "dotenv": "^17.4.2",
-      "zod": "^4.4.3",
-      "lucide-react": "^1.23.0",
-      "next-themes": "^0.4.6",
-      "react": "19.2.8",
-      "react-dom": "19.2.8",
-      "sonner": "^2.0.7",
-      "convex": "^1.42.1",
-      "better-auth": "1.6.15",
-      "@convex-dev/better-auth": "^0.12.5",
-      "@tanstack/react-form": "^1.33.0",
-      "@types/react-dom": "^19.2.3",
-      "tailwindcss": "^4.3.2",
-      "tailwind-merge": "^3.6.0",
-      "@better-auth/expo": "1.6.15",
-      "effect": "4.0.0-beta.99",
-      "typescript": "^6",
-      "@types/bun": "latest",
-      "heroui-native": "^1.0.5",
-      "vite": "^7.3.6",
-      "vitest": "^4.1.10",
-      "convex-test": "^0.0.54",
-      "react-native": "0.86.0",
-      "@types/react": "^19.2.17",
-      "@types/node": "^22.13.14",
-      "hono": "^4.8.3",
-      "valibot": "^1.4.2",
-      "streamdown": "2.5.0",
-      "@tailwindcss/postcss": "^4.3.2",
-      "@tailwindcss/vite": "^4.3.2"
-    }
-  },
   "type": "module",
   "scripts": {
     "dev": "vp run -r dev",
@@ -65,8 +18,8 @@
     "dev:server": "vp run --filter @code/backend dev",
     "dev:setup": "vp run --filter @code/backend dev:setup",
     "build:agents": "vp run --filter @code/agents build",
-    "docs:update": "bun run scripts/update-docs.ts",
-    "subtree": "bun run scripts/subtree.ts",
+    "docs:update": "node scripts/update-docs.ts",
+    "subtree": "node scripts/subtree.ts",
     "fix": "ultracite fix",
     "slice1": "vp run -r dev",
     "dev:zopu": "vp run --filter @code/agents dev",
@@ -92,10 +45,5 @@
     "vite-plus": "0.2.2",
     "vitest": "catalog:"
   },
-  "overrides": {
-    "react": "19.2.8",
-    "react-dom": "19.2.8",
-    "vite": "npm:@voidzero-dev/vite-plus-core@0.2.2"
-  },
-  "packageManager": "bun@1.3.14"
+  "packageManager": "pnpm@11.17.0"
 }

packages/agents/flue.config.ts

@@ -1,5 +1,5 @@
-import { defineConfig } from '@flue/cli/config';
+import { defineConfig } from "@flue/cli/config";
 
 export default defineConfig({
-  target: 'node',
+  target: "node",
 });

packages/agents/package.json

@@ -4,14 +4,15 @@
   "private": true,
   "type": "module",
   "scripts": {
-    "build": "bun --env-file=../../.env flue build",
+    "build": "node --env-file=../../.env node_modules/@flue/cli/bin/flue.mjs build",
+    "start": "node --env-file=../../.env dist/server.mjs",
     "check-types": "tsc --noEmit",
-    "dev": "bun --env-file=../../.env flue dev",
-    "dev:tailscale": "bun --env-file=../../.env flue dev",
-    "run": "bun --env-file=../../.env flue run",
-    "runner": "bun --env-file=../../.env src/runner.ts",
-    "run:zopu": "bun --env-file=../../.env flue run zopu",
-    "run:work-planner": "bun --env-file=../../.env flue run work-planner"
+    "dev": "node --env-file=../../.env node_modules/@flue/cli/bin/flue.mjs dev",
+    "dev:tailscale": "node --env-file=../../.env node_modules/@flue/cli/bin/flue.mjs dev",
+    "run": "node --env-file=../../.env node_modules/@flue/cli/bin/flue.mjs run",
+    "runner": "node --env-file=../../.env src/runner.ts",
+    "run:zopu": "node --env-file=../../.env node_modules/@flue/cli/bin/flue.mjs run zopu",
+    "run:work-planner": "node --env-file=../../.env node_modules/@flue/cli/bin/flue.mjs run work-planner"
   },
   "dependencies": {
     "@agentos-software/git": "0.3.3",
@@ -30,6 +31,10 @@
     "@code/config": "workspace:*",
     "@flue/cli": "latest",
     "@types/bun": "catalog:",
+    "@types/node": "catalog:",
     "typescript": "catalog:"
+  },
+  "engines": {
+    "node": ">=22.18 <23 || >=23.6"
   }
 }

packages/agents/src/agents/zopu.ts

@@ -1,54 +1,9 @@
 import { parseAgentEnv } from "@code/env/agent";
 import { defineAgent } from "@flue/runtime";
 
+import INSTRUCTIONS from "../prompts/zopu-instructions.md" with { type: "markdown" };
 import { createSliceOneTools } from "../tools/slice-one";
 
-const INSTRUCTIONS = `You are Zopu for product Slice 1 and the Work planning handoff.
-
-## Your role
-
-The application stores each user message as exact evidence before you process it. You may interpret that evidence, but never supply, rewrite, or invent source text.
-
-## Work routing loop
-
-When a user sends a message, follow this decision flow:
-
-1. **Assess actionability.** Does the message contain a concrete problem, request, blocker, opportunity, or decision that warrants a work unit? Greetings, questions about the system, casual conversation, and exploration do NOT create work. If the message is casual conversation, respond naturally and do nothing else.
-
-   Direct questions, casual conversation, and image-reading requests must be answered immediately without calling any tools.
-
-2. **Identify project context.** Call list_projects. If there is one project, use it. If there are several and the request is ambiguous, ask one focused question.
-
-3. **Create a Signal (only when actionable).** When the message is actionable:
-   a. Call list_signal_evidence to see the exact admitted user messages.
-   b. Select the message IDs that compose the problem statement.
-   c. Call create_signal with a structured problem statement (title, summary, desiredOutcome, constraints). The problem statement must faithfully represent the user's own intent. Do not invent scope they did not mention.
-   d. Include the projectId when the project is known.
-
-4. **Route the Signal.** After creating the Signal:
-   a. Call list_proposed_work for the project.
-   b. If the Signal clearly describes the same desired outcome as existing Work, call attach_signal_to_work.
-   c. Otherwise call create_work_from_signal.
-   e. If genuinely uncertain whether to attach or create, ask one focused question.
-
-5. **Explain the outcome.** Tell the user clearly what happened:
-   - "Captured [Signal title] and linked it to [Work title]."
-   - "Captured [Signal title] and proposed [Work title]."
-   - Keep the response brief; the product renders the durable Work card separately.
-
-## Rules
-
-- Never supply or rewrite the raw source message text. The control plane copies it server-side.
-- You receive and can see images attached to the current user message. This model supports image input. Never claim images are unavailable, omitted, or unsupported. If a message has attached images, inspect them before responding.
-- Never create Work from casual chat.
-- Ask at most one focused clarification when genuinely ambiguous.
-- Preserve project and organization scope at all times.
-- Repeated delivery of the same message must not create duplicate Signals or attachments. The backend is idempotent.
-- Never claim you created a Signal until the tool call returns successfully.
-- Do not start implementation, planning, sandboxes, Git, verification, or delivery. Those are explicitly outside Slice 1.
-   - After creating proposed Work, the system may invoke the private work-planner. Never claim that a Definition, Design, approval, or implementation exists unless Convex reports it.
-   - Proposed Work is the only Work status you directly create.`;
-
 export {
   convexAgentRoute as attachments,
   convexAgentRoute as route,

packages/agents/src/prompts/zopu-instructions.md

@@ -0,0 +1,45 @@
+You are Zopu for product Slice 1 and the Work planning handoff.
+
+## Your role
+
+The application stores each user message as exact evidence before you process it. You may interpret that evidence, but never supply, rewrite, or invent source text.
+
+## Work routing loop
+
+When a user sends a message, follow this decision flow:
+
+1. **Assess actionability.** Does the message contain a concrete problem, request, blocker, opportunity, or decision that warrants a work unit? Greetings, questions about the system, casual conversation, and exploration do NOT create work. If the message is casual conversation, respond naturally and do nothing else.
+
+   Direct questions, casual conversation, and image-reading requests must be answered immediately without calling any tools.
+
+2. **Identify project context.** Call list_projects. If there is one project, use it. If there are several and the request is ambiguous, ask one focused question.
+
+3. **Create a Signal (only when actionable).** When the message is actionable:
+   a. Call list_signal_evidence to see the exact admitted user messages.
+   b. Select the message IDs that compose the problem statement.
+   c. Call create_signal with a structured problem statement (title, summary, desiredOutcome, constraints). The problem statement must faithfully represent the user's own intent. Do not invent scope they did not mention.
+   d. Include the projectId when the project is known.
+
+4. **Route the Signal.** After creating the Signal:
+   a. Call list_proposed_work for the project.
+   b. If the Signal clearly describes the same desired outcome as existing Work, call attach_signal_to_work.
+   c. Otherwise call create_work_from_signal.
+   e. If genuinely uncertain whether to attach or create, ask one focused question.
+
+5. **Explain the outcome.** Tell the user clearly what happened:
+   - "Captured [Signal title] and linked it to [Work title]."
+   - "Captured [Signal title] and proposed [Work title]."
+   - Keep the response brief; the product renders the durable Work card separately.
+
+## Rules
+
+- Never supply or rewrite the raw source message text. The control plane copies it server-side.
+- You receive and can see images attached to the current user message. This model supports image input. Never claim images are unavailable, omitted, or unsupported. If a message has attached images, inspect them before responding.
+- Never create Work from casual chat.
+- Ask at most one focused clarification when genuinely ambiguous.
+- Preserve project and organization scope at all times.
+- Repeated delivery of the same message must not create duplicate Signals or attachments. The backend is idempotent.
+- Never claim you created a Signal until the tool call returns successfully.
+- Do not start implementation, planning, sandboxes, Git, verification, or delivery. Those are explicitly outside Slice 1.
+   - After creating proposed Work, the system may invoke the private work-planner. Never claim that a Definition, Design, approval, or implementation exists unless Convex reports it.
+   - Proposed Work is the only Work status you directly create.

packages/agents/src/runtime/agent-os.ts

@@ -1,22 +1,20 @@
 import { parseAgentEnv } from "@code/env/agent";
+import {
+  makePiAgentOsConfig,
+  makePiHomeFiles,
+  decodeWorkAttemptExecutionInput,
+  WorkAttemptExecutionError,
+  piSessionEnv,
+} from "@code/primitives";
+import type {
+  ExecutionEvent,
+  WorkAttemptExecutionResult,
+} from "@code/primitives";
 import { agentOS, setup } from "@rivet-dev/agentos";
 import { createHostDirBackend } from "@rivet-dev/agentos-core";
 import { createClient } from "@rivet-dev/agentos/client";
 import { Effect } from "effect";
 
-import {
-  makePiAgentOsConfig,
-  makePiHomeFiles,
-  piSessionEnv,
-} from "../../../primitives/src/agent-os";
-import {
-  decodeWorkAttemptExecutionInput,
-  WorkAttemptExecutionError,
-} from "../../../primitives/src/execution-runtime";
-import type {
-  ExecutionEvent,
-  WorkAttemptExecutionResult,
-} from "../../../primitives/src/execution-runtime";
 import { HostRepositoryWorkspace } from "./host-repository";
 
 const piConfig = makePiAgentOsConfig();
@@ -116,40 +114,53 @@ export const executeAgentOsAttempt = async (
           : "Isolated Zopu worktree recreated"
       )
     );
-    await Promise.all([
-      vm.mountFs({
+    const mounts = [
+      {
+        hostPath: prepared.checkoutPath,
         path: "/workspace/repository",
-        plugin: createHostDirBackend({
-          hostPath: prepared.checkoutPath,
-          readOnly: false,
-        }),
         readOnly: false,
-      }),
-      vm.mountFs({
-        path: `${prepared.sourceRepositoryPath}/.git`,
-        plugin: createHostDirBackend({
-          hostPath: `${prepared.sourceRepositoryPath}/.git`,
-          readOnly: false,
-        }),
+      },
+      {
+        hostPath: prepared.sourceRepositoryPath,
+        path: prepared.sourceRepositoryPath,
         readOnly: false,
-      }),
-      vm.mountFs({
+      },
+      {
+        hostPath: prepared.piHomePath,
         path: "/home/zopu",
-        plugin: createHostDirBackend({
-          hostPath: prepared.piHomePath,
-          readOnly: false,
-        }),
         readOnly: false,
-      }),
-      vm.mountFs({
+      },
+      {
+        hostPath: prepared.toolsPath,
         path: "/opt/zopu-tools",
-        plugin: createHostDirBackend({
-          hostPath: prepared.toolsPath,
-          readOnly: true,
-        }),
         readOnly: true,
-      }),
-    ]);
+      },
+    ] as const;
+    const mountNext = async (index: number): Promise<void> => {
+      const mount = mounts[index];
+      if (!mount) {
+        return;
+      }
+      try {
+        await vm.mountFs({
+          path: mount.path,
+          plugin: createHostDirBackend({
+            hostPath: mount.hostPath,
+            readOnly: mount.readOnly,
+          }),
+          readOnly: mount.readOnly,
+        });
+      } catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        throw executionError(
+          `Failed to mount ${mount.hostPath} at ${mount.path}: ${message}`,
+          "HarnessFailed",
+          false
+        );
+      }
+      await mountNext(index + 1);
+    };
+    await mountNext(0);
     const { baseRevision } = prepared;
     events.push(
       event(2, "repository.ready", "Repository checkout is ready", {

packages/agents/src/runtime/host-repository.ts

@@ -11,7 +11,7 @@ import {
 } from "node:fs/promises";
 import path from "node:path";
 
-import type { PiHomeFiles } from "../../../primitives/src/agent-os";
+import type { PiHomeFiles } from "@code/primitives";
 
 interface PrepareRepositoryInput {
   attemptId: string;
@@ -159,6 +159,10 @@ export class HostRepositoryWorkspace {
       "Zopu worktree creation"
     );
 
+    const bunExecutable =
+      process.env.BUN_EXECUTABLE ??
+      execFileSync("which", ["bun"], { encoding: "utf-8" }).trim();
+
     const sourceEnvPath = path.join(this.#sourceRepositoryPath, ".env");
     if (await pathExists(sourceEnvPath)) {
       await copyFile(sourceEnvPath, path.join(checkoutPath, ".env"));
@@ -166,7 +170,7 @@ export class HostRepositoryWorkspace {
     if (this.#installDependencies) {
       requireSuccess(
         await runProcess(
-          "bun",
+          bunExecutable,
           ["install", "--frozen-lockfile"],
           checkoutPath,
           { CI: "1" }
@@ -177,9 +181,6 @@ export class HostRepositoryWorkspace {
 
     const toolsBinPath = path.join(toolsPath, "bin");
     await mkdir(toolsBinPath, { recursive: true });
-    const bunExecutable = execFileSync("which", ["bun"], {
-      encoding: "utf-8",
-    }).trim();
     const bunPath = path.join(toolsBinPath, "bun");
     await copyFile(bunExecutable, bunPath);
     await chmod(bunPath, 0o755);

pnpm-workspace.yaml

@@ -0,0 +1,62 @@
+packages:
+  - apps/web
+  - packages/agents
+  - packages/auth
+  - packages/backend
+  - packages/config
+  - packages/env
+  - packages/primitives
+  - packages/ui
+
+allowBuilds:
+  "@google/genai": true
+  "@mongodb-js/zstd": true
+  better-sqlite3: true
+  cbor-extract: true
+  esbuild: true
+  isolated-vm: true
+  koffi: true
+  msgpackr-extract: true
+  node-liblzma: true
+  protobufjs: true
+  workerd: true
+
+catalog:
+  "@rivet-dev/agentos": "^0.2.7"
+  "@rivet-dev/agentos-core": "^0.2.10"
+  "@effect/platform-bun": "4.0.0-beta.99"
+  dotenv: "^17.4.2"
+  zod: "^4.4.3"
+  lucide-react: "^1.23.0"
+  next-themes: "^0.4.6"
+  react: "19.2.8"
+  react-dom: "19.2.8"
+  sonner: "^2.0.7"
+  convex: "^1.42.1"
+  better-auth: "1.6.15"
+  "@convex-dev/better-auth": "^0.12.5"
+  "@tanstack/react-form": "^1.33.0"
+  "@types/react-dom": "^19.2.3"
+  tailwindcss: "^4.3.2"
+  tailwind-merge: "^3.6.0"
+  "@better-auth/expo": "1.6.15"
+  effect: "4.0.0-beta.99"
+  typescript: "^7.0.2"
+  "@types/bun": "latest"
+  heroui-native: "^1.0.5"
+  vite: "^7.3.6"
+  vitest: "^4.1.10"
+  convex-test: "^0.0.54"
+  react-native: "0.86.0"
+  "@types/react": "^19.2.17"
+  "@types/node": "^22.13.14"
+  hono: "^4.8.3"
+  valibot: "^1.4.2"
+  streamdown: "2.5.0"
+  "@tailwindcss/postcss": "^4.3.2"
+  "@tailwindcss/vite": "^4.3.2"
+
+overrides:
+  react: 19.2.8
+  react-dom: 19.2.8
+  vite: npm:@voidzero-dev/vite-plus-core@0.2.2