Preserve admitted instruction root across Pi warm turns

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

@@ -441,6 +441,9 @@ export type NativeInstructionWorkingCopy = {
 
 type WarmNativeSession = {
   instructionWorkingCopy?: NativeInstructionWorkingCopy;
+  // Keep the admitted physical root independent of the per-run collection
+  // capability, which instruction preparation adopts before final admission.
+  instructionRoot?: string;
   instructionPreparationRunId?: string;
   agentId: string;
   instructionCopy?: { runId: string; root?: string; targetIdentity: string; collectStopped: () => Promise<void> };
@@ -8445,7 +8448,7 @@ async function executePaperclipNativeSessionWithinScope(
         entry.closeOnReleaseReason !== undefined ||
         entry.configDigest !== warmConfigDigest ||
         entry.configuredEnvironmentDigest !== configuredEnvironmentDigest ||
-        entry.instructionCopy?.root !== input.instructionWorkingCopy?.root ||
+        entry.instructionRoot !== input.instructionWorkingCopy?.root ||
         entry.managedAiCredentialIdentity !== input.managedAiCredentialIdentity ||
         credentialRunChanged ||
         Boolean(entry.githubAccess) !== Boolean(input.managedGitHub) ||
@@ -8839,6 +8842,7 @@ async function executePaperclipNativeSessionWithinScope(
                 } else
                   warmNativeSessions.set(warmSessionId, {
                     instructionWorkingCopy: input.instructionWorkingCopy?.checkpointWarm ? undefined : input.instructionWorkingCopy,
+                    instructionRoot: input.instructionWorkingCopy?.root,
                     agentId: input.execution.binding.agentId,
                     managedAiCredentialIdentity: input.managedAiCredentialIdentity,
                     githubAuthenticationMode: