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/remote-managed-runtime.ts

@@ -5,6 +5,7 @@ import {
   restoreWorkspaceFromSshExecution,
   syncDirectoryToSsh,
 } from "./ssh.js";
+import { captureDirectorySnapshot } from "./workspace-restore-merge.js";
 
 export interface RemoteManagedRuntimeAsset {
   key: string;
@@ -63,19 +64,31 @@ export function remoteExecutionSessionMatches(saved: unknown, current: SshRemote
 
 export async function prepareRemoteManagedRuntime(input: {
   spec: SshRemoteExecutionSpec;
+  runId: string;
   adapterKey: string;
   workspaceLocalDir: string;
   workspaceRemoteDir?: string;
   assets?: RemoteManagedRuntimeAsset[];
 }): Promise<PreparedRemoteManagedRuntime> {
-  const workspaceRemoteDir = input.workspaceRemoteDir ?? input.spec.remoteCwd;
+  const baseWorkspaceRemoteDir = input.workspaceRemoteDir ?? input.spec.remoteCwd;
+  const workspaceRemoteDir = path.posix.join(
+    baseWorkspaceRemoteDir,
+    ".paperclip-runtime",
+    "runs",
+    input.runId,
+    "workspace",
+  );
   const runtimeRootDir = path.posix.join(workspaceRemoteDir, ".paperclip-runtime", input.adapterKey);
 
-  await prepareWorkspaceForSshExecution({
+  const preparedWorkspace = await prepareWorkspaceForSshExecution({
     spec: input.spec,
     localDir: input.workspaceLocalDir,
     remoteDir: workspaceRemoteDir,
   });
+  const restoreExclude = preparedWorkspace.gitBacked ? [".git", ".paperclip-runtime"] : [".paperclip-runtime"];
+  const baselineSnapshot = await captureDirectorySnapshot(input.workspaceLocalDir, {
+    exclude: restoreExclude,
+  });
 
   const assetDirs: Record<string, string> = {};
   try {
@@ -95,6 +108,8 @@ export async function prepareRemoteManagedRuntime(input: {
       spec: input.spec,
       localDir: input.workspaceLocalDir,
       remoteDir: workspaceRemoteDir,
+      baselineSnapshot,
+      restoreGitHistory: preparedWorkspace.gitBacked,
     });
     throw error;
   }
@@ -110,6 +125,8 @@ export async function prepareRemoteManagedRuntime(input: {
         spec: input.spec,
         localDir: input.workspaceLocalDir,
         remoteDir: workspaceRemoteDir,
+        baselineSnapshot,
+        restoreGitHistory: preparedWorkspace.gitBacked,
       });
     },
   };