diff --git a/harnesses/contexts/agent-repo/v1/init.sh b/harnesses/contexts/agent-repo/v1/init.sh
index 36868df..55a0403 100755
--- a/harnesses/contexts/agent-repo/v1/init.sh
+++ b/harnesses/contexts/agent-repo/v1/init.sh
@@ -75,7 +75,7 @@ if [ -n "${AGENT_REPO_URL:-}" ] && [ -n "${AGENT_BRANCH:-}" ]; then
             # finalize.sh to merge into ci_metadata.json (AR-25). Falls back
             # to the legacy inline AR-14a logic if the CLI is unavailable.
             mkdir -p /workspace/.agent-output
-            AR39_OUT=$(python3 -m entrypoint.agent_repo_base select-base \
+            AR39_OUT=$(python3 /opt/agent/agent_repo_base.py select-base \
                 --workdir /workspace/project \
                 --branch "$AGENT_BRANCH" \
                 --upstream-url "${AGENT_UPSTREAM_REPO_URL:-}" \
diff --git a/task-templates/workflow/scope-decompose-sonnet@2.yaml b/task-templates/workflow/scope-decompose-sonnet@2.yaml
index 188e278..ba95dd3 100644
--- a/task-templates/workflow/scope-decompose-sonnet@2.yaml
+++ b/task-templates/workflow/scope-decompose-sonnet@2.yaml
@@ -26,6 +26,8 @@ nodes:
     runtime_env:
       AGENT_REPO_URL: "git@gitea.oreillyit.nz-ai-enablement:skynet/agent-runtimes-agents.git"
       AGENT_BRANCH: "spec/${item.uuid}"
+      AGENT_UPSTREAM_REPO_URL: "git@gitea.oreillyit.nz-ai-enablement:skynet/agent-runtimes.git"
+      AGENT_UPSTREAM_BRANCH: "main"
       CP_URL: "https://agents.oreillyit.nz/api"
       # The deliverable is a directory of plan files on disk — NOT a git diff.
       AGENT_EMPTY_DELIVERABLE_CHECK: "false"