fix(agent-repo): AR-39b run base selector by absolute path; seed scope-decompose@2 from upstream

init.sh invoked 'python3 -m entrypoint.agent_repo_base' from /workspace/project, so a project
repo's own entrypoint/ shadowed the image's and the selector crashed. Invoke the image copy by
path. scope-decompose-sonnet@2 gains AGENT_UPSTREAM_REPO_URL/BRANCH so fresh spec branches seed
from upstream main instead of the stale fork main.

Claude-Session: https://claude.ai/code/session_01N218bERyNeLhbLmDRDvbWF

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:-}" \