diff --git a/.gitignore b/.gitignore
index 32f0e3d..c67c60a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -57,3 +57,7 @@ playwright-report/
 
 # per-machine Tailscale cert for the Vite dev server (`tailscale cert`)
 .certs/
+
+# tanstack sandbox projected state
+.tanstack-projected-*
+data/
diff --git a/src/cli.ts b/src/cli.ts
index a1ff987..d0c1fcf 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -72,6 +72,7 @@ export async function runCli(options: CliOptions): Promise<number> {
     dir: options.dir,
     input: options.input,
     adapter: options.adapter,
+    prepareWorkspace: options.clone !== undefined,
     ...(repo !== undefined ? { repo } : {}),
     onEvent: (event) => {
       console.log(formatEvent(event));
diff --git a/src/lib/clone.ts b/src/lib/clone.ts
index 6c5b894..bc3a91a 100644
--- a/src/lib/clone.ts
+++ b/src/lib/clone.ts
@@ -8,7 +8,6 @@
 import { existsSync } from "node:fs";
 import { rm } from "node:fs/promises";
 import { hostExec } from "./exec";
-import { writeHeadlessPermissions } from "./sandbox-config";
 
 export interface GitIdentity {
   readonly name: string;
@@ -46,7 +45,4 @@ export async function resetClone(
       );
     }
   }
-
-  // Headless permission policy (#24), same as the workspace path.
-  await writeHeadlessPermissions(dir);
 }
diff --git a/src/lib/sandbox-config.test.ts b/src/lib/sandbox-config.test.ts
index 18697df..aef292e 100644
--- a/src/lib/sandbox-config.test.ts
+++ b/src/lib/sandbox-config.test.ts
@@ -2,13 +2,11 @@ import { existsSync, mkdtempSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { describe, expect, test } from "bun:test";
-import { resetClone } from "./clone";
+import { opencodeAdapter } from "../runtime/opencode-adapter";
 
-const IDENTITY = { name: "Test Bot", email: "test@factory.local" };
-
-describe("resetClone (#24 headless permission policy)", () => {
-  test("the legacy clone path writes the same opencode.json policy", async () => {
-    const root = mkdtempSync(join(tmpdir(), "factory-clone-sandbox-config-test-"));
+describe("opencodeAdapter.prepareWorkspace (#24 headless permission policy)", () => {
+  test("writes opencode.json with the never-ask policy and excludes it from staging", async () => {
+    const root = mkdtempSync(join(tmpdir(), "factory-adapter-sandbox-config-test-"));
     const seed = join(root, "seed-repo");
     await Bun.$`git init -b main -q ${seed}`.quiet();
     await Bun.$`echo one > ${join(seed, "seed.txt")}`.quiet();
@@ -16,7 +14,9 @@ describe("resetClone (#24 headless permission policy)", () => {
     await Bun.$`git -C ${seed} -c user.name=seed -c user.email=seed@seed.local commit -q -m seed`.quiet();
 
     const dir = join(root, "run-a");
-    await resetClone(dir, seed, IDENTITY);
+    await Bun.$`git clone -q ${seed} ${dir}`.quiet();
+
+    await opencodeAdapter.prepareWorkspace(dir);
 
     expect(existsSync(join(dir, "opencode.json"))).toBe(true);
     const config = JSON.parse(await Bun.$`cat ${join(dir, "opencode.json")}`.text()) as {
diff --git a/src/lib/sandbox-config.ts b/src/lib/sandbox-config.ts
index e829b16..803da42 100644
--- a/src/lib/sandbox-config.ts
+++ b/src/lib/sandbox-config.ts
@@ -7,8 +7,9 @@
  * ask is a permanent silent deadlock of the run, its WIP slot, and its
  * workspace.
  *
- * `allocateWorkspace`/`resetClone` write `opencode.json` into every run tree
- * with `permission: {"*": "allow"}`, verified against opencode's
+ * ADR 0012 §3 (#37): the opencode adapter calls `writeHeadlessPermissions`
+ * from `prepareWorkspace`, writing `opencode.json` with `permission:
+ * {"*": "allow"}` into every run tree. Verified against opencode's
  * `PermissionConfig` schema (`"*"`, `"allow"`, and every category including
  * `external_directory` are accepted keys). The tree is a throwaway sandbox
  * clone where `gh`/`git` already run host-side; the asks this eliminates are
diff --git a/src/lib/workspace.test.ts b/src/lib/workspace.test.ts
index 5fe93df..dfa8305 100644
--- a/src/lib/workspace.test.ts
+++ b/src/lib/workspace.test.ts
@@ -145,32 +145,6 @@ describe("allocateWorkspace (D28)", () => {
     rmSync(root, { recursive: true, force: true });
   });
 
-  test("the allocated tree carries the headless permission policy (#24), excluded from staging", async () => {
-    const root = mkdtempSync(join(tmpdir(), "factory-workspace-sandbox-config-test-"));
-    const workspaceRoot = join(root, "workspaces");
-    const seed = join(root, "seed-repo");
-    await seedRepo(seed, "one");
-
-    const dir = await allocateWorkspace({
-      runId: "run-a",
-      workspaceRoot,
-      sshUrl: seed,
-      identity: IDENTITY,
-      retainedWorkspaces: 10,
-    });
-
-    const config = JSON.parse(await Bun.$`cat ${join(dir, "opencode.json")}`.text()) as {
-      permission: Record<string, string>;
-    };
-    expect(config.permission).toEqual({ "*": "allow" });
-
-    const untracked = (
-      await Bun.$`git -C ${dir} status --porcelain --untracked-files=all`.text()
-    ).trim();
-    expect(untracked).toBe("");
-    rmSync(root, { recursive: true, force: true });
-  });
-
   test("write-back from an allocated tree pushes to the configured remote, against a bare mirror (H1)", async () => {
     const root = mkdtempSync(join(tmpdir(), "factory-workspace-push-test-"));
     const workspaceRoot = join(root, "workspaces");
diff --git a/src/lib/workspace.ts b/src/lib/workspace.ts
index e0ce4c7..94008f9 100644
--- a/src/lib/workspace.ts
+++ b/src/lib/workspace.ts
@@ -28,7 +28,6 @@ import { join } from "node:path";
 import type { GitIdentity } from "./clone";
 import { hostExec, type ExecFn, type ExecResult } from "./exec";
 import type { WorkspaceKind } from "../workflow";
-import { writeHeadlessPermissions } from "./sandbox-config";
 
 const MIRROR_DIR = ".mirror.git";
 
@@ -149,13 +148,6 @@ export async function allocateWorkspace(input: WorkspaceAllocationInput): Promis
     }
   }
 
-  // Headless permission policy (#24): the sandboxed serve must never park a
-  // turn on a permission ask. Guarded so an injected test fake (which spawns
-  // nothing and therefore leaves `dir` absent) does not fail the allocation.
-  if (existsSync(dir)) {
-    await writeHeadlessPermissions(dir);
-  }
-
   await evictOldWorkspaces(
     workspaceRoot,
     retainedWorkspaces,
diff --git a/src/replay/adapter.ts b/src/replay/adapter.ts
index 6f5a85f..5130bcc 100644
--- a/src/replay/adapter.ts
+++ b/src/replay/adapter.ts
@@ -65,6 +65,8 @@ export function createCorpusReplayAdapter(path: string): AgentAdapter {
   let cursor = 0;
 
   return {
+    async prepareWorkspace(_dir: string): Promise<void> {},
+
     stream(_options: AgentAdapterOptions): AsyncIterable<AgentAdapterYield> {
       const index = cursor;
       cursor += 1;
@@ -95,6 +97,8 @@ export function createCorpusReplayAdapter(path: string): AgentAdapter {
  */
 export function createSlowFakeAdapter(chunks: ReadonlyArray<unknown>, delayMs = 20): AgentAdapter {
   return {
+    async prepareWorkspace(_dir: string): Promise<void> {},
+
     stream(_options: AgentAdapterOptions): AsyncIterable<AgentAdapterYield> {
       return {
         async *[Symbol.asyncIterator]() {
diff --git a/src/runtime/agent-adapter.ts b/src/runtime/agent-adapter.ts
index 5af341a..cd9c064 100644
--- a/src/runtime/agent-adapter.ts
+++ b/src/runtime/agent-adapter.ts
@@ -46,4 +46,11 @@ export interface AgentAdapterYield {
 
 export interface AgentAdapter {
   stream(options: AgentAdapterOptions): AsyncIterable<AgentAdapterYield>;
+  /**
+   * ADR 0012 §3: the adapter prepares its own workspace before the first
+   * agent step. The opencode adapter writes `opencode.json` with a
+   * never-ask permission policy (#24) and excludes it from staging. Other
+   * adapters may no-op (replay, scratch).
+   */
+  prepareWorkspace(dir: string): Promise<void>;
 }
diff --git a/src/runtime/agent-step.test.ts b/src/runtime/agent-step.test.ts
index a33f438..17069d1 100644
--- a/src/runtime/agent-step.test.ts
+++ b/src/runtime/agent-step.test.ts
@@ -9,6 +9,7 @@ function makeYield(chunk: unknown, signal?: AgentSignal): AgentAdapterYield {
 
 function signalAdapter(yields: ReadonlyArray<AgentAdapterYield>) {
   return {
+    async prepareWorkspace(_dir: string): Promise<void> {},
     stream() {
       return {
         async *[Symbol.asyncIterator]() {
diff --git a/src/runtime/agent-step.usage.test.ts b/src/runtime/agent-step.usage.test.ts
index 00e65b4..0031220 100644
--- a/src/runtime/agent-step.usage.test.ts
+++ b/src/runtime/agent-step.usage.test.ts
@@ -28,6 +28,7 @@ async function runBlock(chunks: ReadonlyArray<unknown>) {
     model: "model",
     prompt: "prompt",
     adapter: {
+      async prepareWorkspace(_dir: string): Promise<void> {},
       async *stream(): AsyncGenerator<AgentAdapterYield> {
         for (const chunk of chunks) {
           yield { chunk };
diff --git a/src/runtime/opencode-adapter.ts b/src/runtime/opencode-adapter.ts
index edefb3f..538f9d0 100644
--- a/src/runtime/opencode-adapter.ts
+++ b/src/runtime/opencode-adapter.ts
@@ -21,6 +21,7 @@ import type {
   AgentAdapterYield,
   AgentSignal,
 } from "./agent-adapter";
+import { writeHeadlessPermissions } from "../lib/sandbox-config";
 
 /**
  * Inspect one raw AG-UI chunk for opencode-specific signals. Returns the
@@ -86,6 +87,10 @@ async function freePort(): Promise<number> {
 }
 
 export const opencodeAdapter: AgentAdapter = {
+  async prepareWorkspace(dir: string): Promise<void> {
+    await writeHeadlessPermissions(dir);
+  },
+
   async *stream(options: AgentAdapterOptions): AsyncIterable<AgentAdapterYield> {
     const sandboxDefinition = defineSandbox({
       id: "factory-run",
diff --git a/src/runtime/run.test.ts b/src/runtime/run.test.ts
index 19880b6..637d2ba 100644
--- a/src/runtime/run.test.ts
+++ b/src/runtime/run.test.ts
@@ -11,6 +11,7 @@ import type { RunEvent } from "../events";
 import { defineWorkflow, Schema } from "../workflow";
 import { createSlowFakeAdapter } from "../replay/adapter";
 import { startRun, RunCancelledSignal } from "./run";
+import type { AgentAdapter } from "./agent-adapter";
 
 describe("RunCancelledSignal as TaggedError (#34)", () => {
   test("carries the _tag", () => {
@@ -299,3 +300,55 @@ describe("startRun model precedence (issue #16)", () => {
     );
   });
 });
+
+describe("startRun prepareWorkspace (ADR 0012 §3, #37)", () => {
+  function trackingAdapter(): AgentAdapter & { readonly prepared: Array<string> } {
+    const prepared: Array<string> = [];
+    const inner = createSlowFakeAdapter([]);
+    return {
+      prepared,
+      async prepareWorkspace(dir: string): Promise<void> {
+        prepared.push(dir);
+      },
+      stream: inner.stream.bind(inner),
+    };
+  }
+
+  test("calls adapter.prepareWorkspace when prepareWorkspace is true", async () => {
+    const events: Array<RunEvent> = [];
+    const adapter = trackingAdapter();
+    const workflow = defineWorkflow("prep-clone", {
+      input: Schema.Struct({}),
+      run: async () => ({}),
+    });
+
+    await startRun(workflow, {
+      runId: "run-prep-clone",
+      dir: "/tmp/clone-dir",
+      input: {},
+      adapter,
+      prepareWorkspace: true,
+      onEvent: (event) => events.push(event),
+    }).result;
+
+    expect(adapter.prepared).toEqual(["/tmp/clone-dir"]);
+  });
+
+  test("does not call adapter.prepareWorkspace when prepareWorkspace is absent", async () => {
+    const adapter = trackingAdapter();
+    const workflow = defineWorkflow("prep-scratch", {
+      input: Schema.Struct({}),
+      run: async () => ({}),
+    });
+
+    await startRun(workflow, {
+      runId: "run-prep-scratch",
+      dir: "/tmp/scratch-dir",
+      input: {},
+      adapter,
+      onEvent: () => {},
+    }).result;
+
+    expect(adapter.prepared).toEqual([]);
+  });
+});
diff --git a/src/runtime/run.ts b/src/runtime/run.ts
index 7119c4f..abf9554 100644
--- a/src/runtime/run.ts
+++ b/src/runtime/run.ts
@@ -74,6 +74,13 @@ export interface StartRunOptions {
    * failure message.
    */
   readonly workspaceKind?: WorkspaceKind;
+  /**
+   * ADR 0012 §3 (#37): when true, the runtime calls `adapter.prepareWorkspace`
+   * before the workflow runs. The caller sets this when it allocated a clone
+   * workspace (daemon's `allocateWorkspace` or legacy `resetClone`). Absent,
+   * no preparation happens (explicit caller-managed dirs, scratch).
+   */
+  readonly prepareWorkspace?: boolean;
   /**
    * The context service behind `ctx.dispatch` (issue #14). Absent, the ctx
    * member is still present but throws — in-process execution is legacy and
@@ -478,6 +485,10 @@ export function startRun<I, O>(
     });
 
     try {
+      if (options.prepareWorkspace === true) {
+        await options.adapter.prepareWorkspace(options.dir);
+      }
+
       const output = await workflow.run(ctx, decodedInput);
 
       if (workflow.output !== undefined) {
diff --git a/src/server/http.ts b/src/server/http.ts
index 1088e3c..26ea22e 100644
--- a/src/server/http.ts
+++ b/src/server/http.ts
@@ -457,6 +457,9 @@ export function createHandler(options: ServerOptions): (req: Request) => Promise
         input: body.input,
         adapter: options.adapter,
         ...(typeof body.dedupeKey === "string" ? { dedupeKey: body.dedupeKey } : {}),
+        ...(body.clone !== undefined && typeof body.dir === "string"
+          ? { prepareWorkspace: true }
+          : {}),
       };
       let runId: string;
       try {
diff --git a/src/server/runs.ts b/src/server/runs.ts
index 3f37c41..5ad9653 100644
--- a/src/server/runs.ts
+++ b/src/server/runs.ts
@@ -160,6 +160,13 @@ export interface StartTrackedRunOptions {
    * through to the run's model precedence chain.
    */
   readonly agentOverrides?: { readonly model?: string };
+  /**
+   * ADR 0012 §3 (#37): when true, the runtime calls `adapter.prepareWorkspace`
+   * before the workflow runs. The caller sets this when it has done a
+   * `resetClone` on `dir`. Combined with the daemon's own allocation check,
+   * this covers both clone paths.
+   */
+  readonly prepareWorkspace?: boolean;
 }
 
 /**
@@ -368,6 +375,8 @@ export async function startTrackedRun(
       dir,
       ...(options.repo !== undefined ? { repo: options.repo } : {}),
       workspaceKind: kind,
+      prepareWorkspace:
+        options.prepareWorkspace === true || (workspaceAllocated && kind === "clone"),
       ...(dispatch !== undefined ? { dispatch } : {}),
       ...(options.parentRunId !== undefined ? { parentRunId: options.parentRunId } : {}),
       ...(options.dedupeKey !== undefined ? { dedupeKey: options.dedupeKey } : {}),