fix: preserve sandbox credentials and Git state across restarts

Park idle native sandbox sessions before app shutdown, adopt retained legacy workspaces without restaging Git, and carry explicitly bound GitHub access through both OpenCode launch filters.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

server/src/services/native-runtime/native-session-executor.ts

@@ -272,6 +272,7 @@ type WarmNativeSession = {
   configDigest: string;
   companyId: string;
   environmentId: string | null;
+  sandbox: boolean;
   busy: boolean;
   idleTimer: ReturnType<typeof setTimeout> | null;
   lastActivityAt: string;
@@ -315,6 +316,37 @@ export async function closeWarmNativeSessionsForEnvironment(input: {
   return { closed, busy, failed };
 }
 
+/** Park idle sandbox sessions while their host still has database and transport
+ * access. Active turns retain their existing restart/reattach contract. */
+export async function closeIdleSandboxNativeSessionsForShutdown(input: {
+  reason: string;
+}): Promise<{ closed: number; busy: number; failed: number }> {
+  const result = { closed: 0, busy: 0, failed: 0 };
+  const pending: WarmNativeSession[] = [];
+  for (const [sessionId, entry] of warmNativeSessions) {
+    if (!entry.sandbox) continue;
+    if (entry.busy) {
+      result.busy += 1;
+      continue;
+    }
+    if (entry.idleTimer !== null) clearTimeout(entry.idleTimer);
+    // Fence every selected owner before the first asynchronous close.
+    warmNativeSessions.delete(sessionId);
+    pending.push(entry);
+  }
+  await Promise.all(Array.from({ length: Math.min(4, pending.length) }, async () => {
+    for (let entry = pending.shift(); entry; entry = pending.shift()) {
+      try {
+        await entry.session.close({ reason: input.reason });
+        result.closed += 1;
+      } catch {
+        result.failed += 1;
+      }
+    }
+  }));
+  return result;
+}
+
 function readBoundedNativeFile(
   path: string,
   maxBytes: number,
@@ -4528,6 +4560,9 @@ async function executePaperclipNativeSessionWithinScope(
                     companyId: input.execution.binding.companyId,
                     environmentId:
                       input.runnerExecutionTarget?.environmentId ?? null,
+                    sandbox:
+                      input.runnerExecutionTarget?.kind === "remote" &&
+                      input.runnerExecutionTarget.transport === "sandbox",
                     busy: true,
                     idleTimer: null,
                     lastActivityAt: new Date().toISOString(),