Harden remote workspace sync and restore flows (#5444)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - When an agent runs against a remote target, Paperclip syncs the
workspace out to the remote at run start and restores changes back to
the local workspace at run end
> - The previous restore flow naïvely overwrote local files with
whatever the remote returned, so files that the remote run never touched
but had timestamp/mode drift could be needlessly rewritten — and a
single static `refs/paperclip/ssh-sync/imported` ref made concurrent SSH
workspace exports race on the same git ref
> - This pull request adds a `workspace-restore-merge` module that diffs
a pre-run snapshot against the post-run remote state and only writes
back files the remote actually changed; SSH workspace exports now use a
per-import unique ref so concurrent runs can't trample each other
> - Every adapter's execute path threads the snapshot through
`prepareAdapterExecutionTargetRuntime` so the merge has the baseline it
needs
> - The benefit is workspace restores no longer churn untouched files,
and concurrent SSH runs no longer collide on the import ref

## What Changed

- `packages/adapter-utils/src/workspace-restore-merge.{ts,test.ts}`: new
module — directory snapshot (kind/mode/sha256/symlink target) plus
snapshot-aware merge that writes only the files the remote changed
- `packages/adapter-utils/src/ssh.ts`: SSH workspace export uses a
per-import unique ref (`refs/paperclip/ssh-sync/imported/<uuid>`);
restore goes through the new merge helper; `ssh-fixture.test.ts` covers
the unique-ref + merge paths
- `packages/adapter-utils/src/sandbox-managed-runtime.ts` +
`remote-managed-runtime.ts`: thread the snapshot/merge through the
sandbox and SSH paths
- `packages/adapter-utils/src/server-utils.{ts,test.ts}` +
`execution-target.ts`: helpers for capturing the pre-run snapshot;
`prepareAdapterExecutionTargetRuntime` gains required `runId` and
optional `workspaceRemoteDir`, and returns the realized
`workspaceRemoteDir`
- Each adapter's `execute.ts` (acpx, claude, codex, cursor, gemini,
opencode, pi) takes the snapshot at run start and passes it through to
the runtime restore
- Remote execute test mocks updated to match the new
`prepareWorkspaceForSshExecution` return shape and the per-run
`${managedRemoteWorkspace}` cwd subdirectory

## Verification

- `pnpm vitest run --no-coverage --project @paperclipai/adapter-utils
--project @paperclipai/adapter-acpx-local --project
@paperclipai/adapter-claude-local --project
@paperclipai/adapter-codex-local --project
@paperclipai/adapter-cursor-local --project
@paperclipai/adapter-gemini-local --project
@paperclipai/adapter-opencode-local --project
@paperclipai/adapter-pi-local` — 196/196 passing
- `pnpm typecheck` clean across the workspace

## Risks

Medium. The restore path now writes a strict subset of what it
previously did — files the remote did not touch are no longer rewritten.
If any flow was relying on a touch-without-content-change being copied
back (timestamp or permission propagation only), that behavior is now
skipped. Snapshot capture adds an O(N-files-in-workspace) hash pass at
run start; the cost is bounded by the existing exclude list. The `runId`
parameter on `prepareAdapterExecutionTargetRuntime` is now required —
every in-tree caller is updated; out-of-tree adapter authors need to
pass it.

## Model Used

Claude Opus 4.7 (1M context)

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable — new module +
every adapter execute path covered
- [x] If this change affects the UI, I have included before/after
screenshots — N/A (no UI)
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

packages/adapter-utils/src/server-utils.test.ts

@@ -9,11 +9,13 @@ import {
   buildInvocationEnvForLogs,
   DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE,
   materializePaperclipSkillCopy,
+  refreshPaperclipWorkspaceEnvForExecution,
   renderPaperclipWakePrompt,
   runningProcesses,
   runChildProcess,
   sanitizeSshRemoteEnv,
   shapePaperclipWorkspaceEnvForExecution,
+  rewriteWorkspaceCwdEnvVarsForExecution,
   stringifyPaperclipWakePayload,
 } from "./server-utils.js";
 
@@ -810,6 +812,99 @@ describe("shapePaperclipWorkspaceEnvForExecution", () => {
   });
 });
 
+describe("rewriteWorkspaceCwdEnvVarsForExecution", () => {
+  it("rewrites custom *_WORKSPACE_CWD env vars for remote execution", () => {
+    const env = rewriteWorkspaceCwdEnvVarsForExecution({
+      workspaceCwd: "/host/workspace",
+      executionCwd: "/remote/workspace",
+      executionTargetIsRemote: true,
+      env: {
+        QA_PROJECT_WORKSPACE_CWD: "/host/workspace",
+        RANDOM_WORKSPACE_CWD: "/host/workspace",
+        OTHER_ENV: "/host/workspace",
+      },
+    });
+
+    expect(env).toEqual({
+      QA_PROJECT_WORKSPACE_CWD: "/remote/workspace",
+      RANDOM_WORKSPACE_CWD: "/remote/workspace",
+      OTHER_ENV: "/host/workspace",
+    });
+  });
+
+  it("does not rewrite matching values for local execution", () => {
+    const env = rewriteWorkspaceCwdEnvVarsForExecution({
+      workspaceCwd: "/host/workspace",
+      executionCwd: "/remote/workspace",
+      executionTargetIsRemote: false,
+      env: {
+        QA_PROJECT_WORKSPACE_CWD: "/host/workspace",
+        RANDOM_WORKSPACE_CWD_TOKEN: "/host/workspace",
+      },
+    });
+
+    expect(env).toEqual({
+      QA_PROJECT_WORKSPACE_CWD: "/host/workspace",
+      RANDOM_WORKSPACE_CWD_TOKEN: "/host/workspace",
+    });
+  });
+});
+
+describe("refreshPaperclipWorkspaceEnvForExecution", () => {
+  it("rewrites Paperclip workspace env to the prepared remote runtime cwd", () => {
+    const env: Record<string, string> = {
+      PAPERCLIP_WORKSPACE_CWD: "/remote/workspace",
+      PAPERCLIP_WORKSPACE_WORKTREE_PATH: "/host/worktree",
+      PAPERCLIP_WORKSPACES_JSON: JSON.stringify([
+        { workspaceId: "workspace-1", cwd: "/remote/workspace" },
+        { workspaceId: "workspace-2", cwd: "/tmp/other" },
+      ]),
+      QA_PROJECT_WORKSPACE_CWD: "/remote/workspace",
+    };
+
+    const shaped = refreshPaperclipWorkspaceEnvForExecution({
+      env,
+      envConfig: {
+        QA_PROJECT_WORKSPACE_CWD: "/host/workspace",
+      },
+      workspaceCwd: "/host/workspace",
+      workspaceWorktreePath: "/host/worktree",
+      workspaceHints: [
+        { workspaceId: "workspace-1", cwd: "/host/workspace" },
+        { workspaceId: "workspace-2", cwd: "/tmp/other" },
+      ],
+      executionTargetIsRemote: true,
+      executionCwd: "/remote/workspace/.paperclip-runtime/runs/run-1/workspace",
+    });
+
+    expect(shaped).toEqual({
+      workspaceCwd: "/remote/workspace/.paperclip-runtime/runs/run-1/workspace",
+      workspaceWorktreePath: null,
+      workspaceHints: [
+        {
+          workspaceId: "workspace-1",
+          cwd: "/remote/workspace/.paperclip-runtime/runs/run-1/workspace",
+        },
+        {
+          workspaceId: "workspace-2",
+        },
+      ],
+    });
+    expect(env.PAPERCLIP_WORKSPACE_CWD).toBe("/remote/workspace/.paperclip-runtime/runs/run-1/workspace");
+    expect(env.PAPERCLIP_WORKSPACE_WORKTREE_PATH).toBeUndefined();
+    expect(env.QA_PROJECT_WORKSPACE_CWD).toBe("/remote/workspace/.paperclip-runtime/runs/run-1/workspace");
+    expect(JSON.parse(env.PAPERCLIP_WORKSPACES_JSON ?? "[]")).toEqual([
+      {
+        workspaceId: "workspace-1",
+        cwd: "/remote/workspace/.paperclip-runtime/runs/run-1/workspace",
+      },
+      {
+        workspaceId: "workspace-2",
+      },
+    ]);
+  });
+});
+
 describe("appendWithByteCap", () => {
   it("keeps valid UTF-8 when trimming through multibyte text", () => {
     const output = appendWithByteCap("prefix ", "hello — world", 7);