Add pipeline-owned publish_reason metadata and surface it in index_repository responses when incremental indexing falls back to containment. The reason is set on existing exact-route skip/fallback paths and cleared on exact publish/full run reset, so MCP and CLI JSON callers can distinguish a safe containment rebuild from an opaque incremental result.
Update the affected-frontier benchmark harness to prefer structured publish_reason while keeping stderr parsing for older binaries. Add focused pipeline assertions and an MCP tool test for incremental_containment with missing_existing_ownership.
Validated with git diff --check, bash scripts/check-source-safety.sh, bash scripts/test-source-safety.sh, python3 -m py_compile scripts/benchmark-incremental-speed.py, escalated make -j8 -f Makefile.cbm build/c/test-runner, escalated CBM_ONLY_SUITE=pipeline build/c/test-runner, escalated CBM_ONLY_SUITE=mcp build/c/test-runner, escalated make -j8 -f Makefile.cbm cbm, and escalated persistent MCP affected-frontier matrix 8/8 pass.
Signed-off-by: Andrew Hundt <ATHundt@gmail.com>
Andrew Hundt
ec83b08c2e