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/execution-target.ts

@@ -67,6 +67,7 @@ export type AdapterManagedRuntimeAsset = RemoteManagedRuntimeAsset;
 
 export interface PreparedAdapterExecutionTargetRuntime {
   target: AdapterExecutionTarget;
+  workspaceRemoteDir: string | null;
   runtimeRootDir: string | null;
   assetDirs: Record<string, string>;
   restoreWorkspace(): Promise<void>;
@@ -167,6 +168,33 @@ export function adapterExecutionTargetRemoteCwd(
   return target?.kind === "remote" ? target.remoteCwd : localCwd;
 }
 
+export function overrideAdapterExecutionTargetRemoteCwd(
+  target: AdapterExecutionTarget | null | undefined,
+  remoteCwd: string | null | undefined,
+): AdapterExecutionTarget | null | undefined {
+  const nextRemoteCwd = remoteCwd?.trim();
+  if (!target || target.kind !== "remote" || !nextRemoteCwd) {
+    return target;
+  }
+  if (target.remoteCwd === nextRemoteCwd) {
+    return target;
+  }
+  if (target.transport === "ssh") {
+    return {
+      ...target,
+      remoteCwd: nextRemoteCwd,
+      spec: {
+        ...target.spec,
+        remoteCwd: nextRemoteCwd,
+      },
+    };
+  }
+  return {
+    ...target,
+    remoteCwd: nextRemoteCwd,
+  };
+}
+
 export function resolveAdapterExecutionTargetCwd(
   target: AdapterExecutionTarget | null | undefined,
   configuredCwd: string | null | undefined,
@@ -858,9 +886,11 @@ export function readAdapterExecutionTarget(input: {
 }
 
 export async function prepareAdapterExecutionTargetRuntime(input: {
+  runId: string;
   target: AdapterExecutionTarget | null | undefined;
   adapterKey: string;
   workspaceLocalDir: string;
+  workspaceRemoteDir?: string;
   workspaceExclude?: string[];
   preserveAbsentOnRestore?: string[];
   assets?: AdapterManagedRuntimeAsset[];
@@ -872,6 +902,7 @@ export async function prepareAdapterExecutionTargetRuntime(input: {
   if (target.kind === "local") {
     return {
       target,
+      workspaceRemoteDir: null,
       runtimeRootDir: null,
       assetDirs: {},
       restoreWorkspace: async () => {},
@@ -881,12 +912,15 @@ export async function prepareAdapterExecutionTargetRuntime(input: {
   if (target.transport === "ssh") {
     const prepared = await prepareRemoteManagedRuntime({
       spec: target.spec,
+      runId: input.runId,
       adapterKey: input.adapterKey,
       workspaceLocalDir: input.workspaceLocalDir,
+      workspaceRemoteDir: input.workspaceRemoteDir,
       assets: input.assets,
     });
     return {
       target,
+      workspaceRemoteDir: prepared.workspaceRemoteDir,
       runtimeRootDir: prepared.runtimeRootDir,
       assetDirs: prepared.assetDirs,
       restoreWorkspace: prepared.restoreWorkspace,
@@ -904,6 +938,7 @@ export async function prepareAdapterExecutionTargetRuntime(input: {
     },
     adapterKey: input.adapterKey,
     workspaceLocalDir: input.workspaceLocalDir,
+    workspaceRemoteDir: input.workspaceRemoteDir,
     workspaceExclude: input.workspaceExclude,
     preserveAbsentOnRestore: input.preserveAbsentOnRestore,
     assets: input.assets,
@@ -912,6 +947,7 @@ export async function prepareAdapterExecutionTargetRuntime(input: {
   });
   return {
     target,
+    workspaceRemoteDir: prepared.workspaceRemoteDir,
     runtimeRootDir: prepared.runtimeRootDir,
     assetDirs: prepared.assetDirs,
     restoreWorkspace: prepared.restoreWorkspace,