[lee-phys]

With selected #4470 at main 6044f37b1f75a57f5fea6d17077b6985893062c1, running python3 -B scripts/research_baseline_sparse.py fails with ValueError: Invalid selected file: certificates/LICENSE. Its explicit repository-files-sha256-v1 inventory contains repository-relative paths, but the preflight treats them as relative to the manifest directory. It also directs productive-helper certificates to the historical balanced-transfer baseline.

This focused change:

• treats explicit file inventories as repository-relative, alongside the existing package inventory format;
• reads the certificate through the same guarded working-tree/HEAD metadata path used for an omitted manifest;
• recommends research_selected_baseline.py for its supported productive-helper schema, including when the certificate is sparsely omitted, and exposes next in both preflight outcomes;
• preserves legacy relative manifests, the historical baseline recommendation for historical certificates, and rejection of ordinary deletions or changed sparse index entries.

Three new real-Git regression cases cover a complete explicit inventory, a non-cone sparse checkout with both metadata files omitted and successful materialization, and a productive certificate using the older package inventory format. All three failed before the implementation change.

Validation on macOS, Python 3.12.13 / Git 2.50.1:

• python3.12 -B -m unittest discover -s tests -p 'test_research_baseline_sparse.py' -v: 8 passed.
• python3.12 -B -m unittest discover -s tests -p 'test_research_selected_baseline.py' -v: 13 passed.
• CI's onboarding command, python3.12 -B -m unittest discover -s tests -p 'test_research_*.py' -v: 334 tests, 316 passed and 18 platform-dependent skips, in 239.227 seconds.
• The current sparse checkout now reports 493 genuine omitted inputs, exit 2, a materialization command and the schema-compatible baseline, instead of inventing certificates/LICENSE.
• git diff --check passed. python3 -B scripts/research_package.py --changed-since 6044f37b1f75a57f5fea6d17077b6985893062c1 --matrix-batch-size 256 selects zero registered replay packages.

Scope: this is a read-only onboarding preflight, not source-hash verification, a scientific replay or a new κ claim. The selected record, pinned baseline implementations and frozen evidence are unchanged. The full selected mathematical replay and native Windows cases were not run.

Task context: portable-replay, priority revision 7, narrowed to selected-baseline onboarding compatibility. Started this fix from canonical main 6044f37b1f75a57f5fea6d17077b6985893062c1; refreshed upstream to fbc9ea0249746acca4f504d4fda2b84e0e36cf0d before submission and checked its sole integration-receipt change. Refreshed overlap evidence covers 405 open PR bodies and 3,574 Discussion records; the 404-PR path snapshot found no matching change, and the newly opened #4629 was checked separately. Historical #376/#473 file inventories are incomplete and 5,824 sparse local notes were outside coverage, so this is not an exhaustive novelty claim.

Credit: Douglas Colkitt and Claude Opus 5.5 for the existing preflight; Arham-Tahir64's #3102 sparse-omission contract; Mihir Srivastava with OpenAI Codex assistance for the productive-helper baseline. The selected #4470 supplier and all inherited notices retain their attribution. This contribution was prepared by lee-phys with substantial OpenAI Codex assistance under Apache-2.0.