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/workspace-restore-merge.test.ts

@@ -0,0 +1,61 @@
+import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+
+import { captureDirectorySnapshot, mergeDirectoryWithBaseline } from "./workspace-restore-merge.js";
+
+describe("workspace restore merge", () => {
+  const cleanupDirs: string[] = [];
+
+  afterEach(async () => {
+    while (cleanupDirs.length > 0) {
+      const dir = cleanupDirs.pop();
+      if (!dir) continue;
+      await rm(dir, { recursive: true, force: true }).catch(() => undefined);
+    }
+  });
+
+  it("preserves sibling files when sequential stale-baseline restores create the same nested directory tree", async () => {
+    const rootDir = await mkdtemp(path.join(os.tmpdir(), "paperclip-restore-merge-"));
+    cleanupDirs.push(rootDir);
+
+    const targetDir = path.join(rootDir, "target");
+    const sourceADir = path.join(rootDir, "source-a");
+    const sourceBDir = path.join(rootDir, "source-b");
+    await mkdir(targetDir, { recursive: true });
+    await mkdir(path.join(sourceADir, "manual-qa", "environment-matrix", "ssh"), { recursive: true });
+    await mkdir(path.join(sourceBDir, "manual-qa", "environment-matrix", "ssh"), { recursive: true });
+
+    const baseline = await captureDirectorySnapshot(targetDir, { exclude: [] });
+
+    await writeFile(
+      path.join(sourceADir, "manual-qa", "environment-matrix", "ssh", "claude_local.md"),
+      "ssh claude\n",
+      "utf8",
+    );
+    await writeFile(
+      path.join(sourceBDir, "manual-qa", "environment-matrix", "ssh", "codex_local.md"),
+      "ssh codex\n",
+      "utf8",
+    );
+
+    await mergeDirectoryWithBaseline({
+      baseline,
+      sourceDir: sourceADir,
+      targetDir,
+    });
+    await mergeDirectoryWithBaseline({
+      baseline,
+      sourceDir: sourceBDir,
+      targetDir,
+    });
+
+    await expect(
+      readFile(path.join(targetDir, "manual-qa", "environment-matrix", "ssh", "claude_local.md"), "utf8"),
+    ).resolves.toBe("ssh claude\n");
+    await expect(
+      readFile(path.join(targetDir, "manual-qa", "environment-matrix", "ssh", "codex_local.md"), "utf8"),
+    ).resolves.toBe("ssh codex\n");
+  });
+});