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/adapters/opencode-local/src/server/execute.remote.test.ts

@@ -45,7 +45,7 @@ const {
   }),
   ensureCommandResolvable: vi.fn(async () => undefined),
   resolveCommandForLogs: vi.fn(async () => "ssh://fixture@127.0.0.1:2222/remote/workspace :: opencode"),
-  prepareWorkspaceForSshExecution: vi.fn(async () => undefined),
+  prepareWorkspaceForSshExecution: vi.fn(async () => ({ gitBacked: false })),
   restoreWorkspaceFromSshExecution: vi.fn(async () => undefined),
   runSshCommand: vi.fn(async () => ({
     stdout: "/home/agent",
@@ -117,6 +117,7 @@ describe("opencode remote execution", () => {
     cleanupDirs.push(rootDir);
     const workspaceDir = path.join(rootDir, "workspace");
     const alternateWorkspaceDir = path.join(rootDir, "workspace-other");
+    const managedRemoteWorkspace = "/remote/workspace/.paperclip-runtime/runs/run-1/workspace";
     await mkdir(workspaceDir, { recursive: true });
     await mkdir(alternateWorkspaceDir, { recursive: true });
 
@@ -176,22 +177,22 @@ describe("opencode remote execution", () => {
 
     expect(result.sessionParams).toMatchObject({
       sessionId: "session_123",
-      cwd: "/remote/workspace",
+      cwd: managedRemoteWorkspace,
       remoteExecution: {
         transport: "ssh",
         host: "127.0.0.1",
         port: 2222,
         username: "fixture",
-        remoteCwd: "/remote/workspace",
+        remoteCwd: managedRemoteWorkspace,
       },
     });
     expect(prepareWorkspaceForSshExecution).toHaveBeenCalledTimes(1);
     expect(syncDirectoryToSsh).toHaveBeenCalledTimes(2);
     expect(syncDirectoryToSsh).toHaveBeenCalledWith(expect.objectContaining({
-      remoteDir: "/remote/workspace/.paperclip-runtime/opencode/xdgConfig",
+      remoteDir: `${managedRemoteWorkspace}/.paperclip-runtime/opencode/xdgConfig`,
     }));
     expect(syncDirectoryToSsh).toHaveBeenCalledWith(expect.objectContaining({
-      remoteDir: "/remote/workspace/.paperclip-runtime/opencode/skills",
+      remoteDir: `${managedRemoteWorkspace}/.paperclip-runtime/opencode/skills`,
       followSymlinks: true,
     }));
     expect(runSshCommand).toHaveBeenCalledWith(
@@ -206,18 +207,22 @@ describe("opencode remote execution", () => {
       | [string, string, string[], { env: Record<string, string>; remoteExecution?: { remoteCwd: string } | null }]
       | undefined;
     expect(modelProbeCall?.[2]).toEqual(["models"]);
+    // The model probe runs after the runtime workspace is prepared (so XDG
+    // points at the managed subdirectory) but the SSH session targets the
+    // original target remoteCwd — the per-run subdirectory is layered
+    // underneath via XDG/runtime config rather than by switching the cwd.
     expect(modelProbeCall?.[3].env.XDG_CONFIG_HOME).toBe(
-      "/remote/workspace/.paperclip-runtime/opencode/xdgConfig",
+      `${managedRemoteWorkspace}/.paperclip-runtime/opencode/xdgConfig`,
     );
     expect(modelProbeCall?.[3].remoteExecution?.remoteCwd).toBe("/remote/workspace");
     const call = runCall as
       | [string, string, string[], { env: Record<string, string>; remoteExecution?: { remoteCwd: string } | null }]
       | undefined;
-    expect(call?.[3].env.PAPERCLIP_WORKSPACE_CWD).toBe("/remote/workspace");
+    expect(call?.[3].env.PAPERCLIP_WORKSPACE_CWD).toBe(managedRemoteWorkspace);
     expect(JSON.parse(call?.[3].env.PAPERCLIP_WORKSPACES_JSON ?? "[]")).toEqual([
       {
         workspaceId: "workspace-1",
-        cwd: "/remote/workspace",
+        cwd: managedRemoteWorkspace,
         repoUrl: "https://github.com/paperclipai/paperclip.git",
         repoRef: "main",
       },
@@ -229,8 +234,8 @@ describe("opencode remote execution", () => {
     ]);
     expect(call?.[3].env.PAPERCLIP_API_URL).toBe("http://127.0.0.1:4310");
     expect(call?.[3].env.PAPERCLIP_API_BRIDGE_MODE).toBe("queue_v1");
-    expect(call?.[3].env.XDG_CONFIG_HOME).toBe("/remote/workspace/.paperclip-runtime/opencode/xdgConfig");
-    expect(call?.[3].remoteExecution?.remoteCwd).toBe("/remote/workspace");
+    expect(call?.[3].env.XDG_CONFIG_HOME).toBe(`${managedRemoteWorkspace}/.paperclip-runtime/opencode/xdgConfig`);
+    expect(call?.[3].remoteExecution?.remoteCwd).toBe(managedRemoteWorkspace);
     expect(startAdapterExecutionTargetPaperclipBridge).toHaveBeenCalledTimes(1);
     expect(restoreWorkspaceFromSshExecution).toHaveBeenCalledTimes(1);
   });
@@ -302,6 +307,7 @@ describe("opencode remote execution", () => {
     const rootDir = await mkdtemp(path.join(os.tmpdir(), "paperclip-opencode-remote-resume-"));
     cleanupDirs.push(rootDir);
     const workspaceDir = path.join(rootDir, "workspace");
+    const managedRemoteWorkspace = "/remote/workspace/.paperclip-runtime/runs/run-ssh-resume/workspace";
     await mkdir(workspaceDir, { recursive: true });
 
     await execute({
@@ -317,13 +323,13 @@ describe("opencode remote execution", () => {
         sessionId: "session-123",
         sessionParams: {
           sessionId: "session-123",
-          cwd: "/remote/workspace",
+          cwd: managedRemoteWorkspace,
           remoteExecution: {
             transport: "ssh",
             host: "127.0.0.1",
             port: 2222,
             username: "fixture",
-            remoteCwd: "/remote/workspace",
+            remoteCwd: managedRemoteWorkspace,
           },
         },
         sessionDisplayId: "session-123",