task: R01 — retire legacy root paths and close core dependencies #412

Current delivery decision (2026-11-15)

Split legacy-path retirement and actual dependency closure into three bounded implementation PRs. Retire already-migrated old paths early instead of keeping every shell until the last integration change. Moving implementation, migrating active consumers/docs/tests and deleting old root modules belong in the same PR. Overall isolation is a real-tree result, not an issue-status or merge inference. This issue closes root-level scattering, old entrypoints and core dependency boundaries; it does not promise internal refactors of existing subpackages.

Related: #387, #371, Apps migration #408, shared contracts/resources #451, and Apps-only MindIE relocation #452.

PR checklist

• R1 — Retire existing legacy root paths and finish canonical inspection binding. Delete the seven Knowledge shells (_skill_selection, _source_snapshot, catalog, knowledge_operations, knowledge_store, research, skill_catalog), the three B01 root paths (evaluation, execution, reporting), and root inspection. In this same PR update all active consumers, including the CLI/arguments if they have not moved yet, tools/current tests/docs, the manifest and affected protected-path rules. Root inspection is not a trivial alias: first preserve its command/snapshot/repository-identity binding in the canonical Apps composition at apps/inspection.py over the existing infra facts API. Do not delete behavior or injection assertions. Maintain the shrinking exact root-file inventory introduced in C1. If R1 is scheduled earlier, record its removals so that C1 initializes the guard from the real tree; R1 does not need a second root guard. When catalog is retired, consumers take REPO_TYPES from resources.repository_packs as the same object (identity assertion), never a copy. Record the exact remaining compatibility pairs at each step: the eight root-shell pairs disappear with the seven shells, and the neutral-leaf importer (infra.inspection -> resources.repository_packs after C2) must be covered by a permanent rule outside compatibility_pairs, with a negative test that only that exact edge is allowed. Leaving it in compatibility_pairs keeps allowlist: 1 in first_wave_report() and makes the final blockers == () unreachable.
• R2 — Close artifact-primitive dependencies in six Harness modules. Remove the infra.artifacts reachability from agent_sessions, candidates, optimization, optimization_session, project and task_protocol, using equivalent Harness-owned primitives or explicit suitable ports. Preserve writer/digest/hash/lock bytes, atomicity, failure and platform semantics. The existing report has 12 path hits from these six modules, not 12 modules: each module carries both the package-level inferrsi.infra edge and the inferrsi.infra.artifacts edge, so removing both is the completion bar; replacing them with imports of other inferrsi.infra modules does not count. The same PR also verifies that Harness has no inferrsi.model edge (the current tree has none); the final gate counts both inferrsi.infra and inferrsi.model.
• R3 — Close five real execution boundaries and prove the combined tree. Handle harness/task_protocol.py, the moe-forward-npu benchmark/grader, qwen21-denoise-npu benchmark and qwen3-tts-npu benchmark through legitimate bounded execution/host interfaces. Preserve candidate/sandbox/integrity controls and frozen input semantics. This PR contains real boundary fixes and final integration acceptance; do not create a ninth verification-only PR.

Dependencies and merge discipline

R1 has no hard prerequisite on C1/C2 (#451) or A1 (#408): deleting existing legacy paths does not itself require relocating a neutral resource leaf first. Prefer C1 → C2 → R1 in the serial queue to avoid rewriting contract/resource policy twice; do not wait for A1/A2/M1 to retire the existing eleven paths. C2 does require the contracts package delivered by C1. Start the shrinking root-file inventory guard in C1, then update its exact set here and in every removal PR. The final two-file target is checked only after the actual remaining moves.

R2 is logically independent and may be scheduled earlier if useful, but only one Claude implementation session runs at once. R2 and R3 both touch task_protocol; R3 must integrate R2's actual head. R3 implementation planning can start earlier, but its final integration/tested head must contain all accepted C/A/M/R predecessor changes. Do not represent a planned DAG as authorization for parallel coding sessions.

Acceptance

• R1 really removes the eleven paths, updates all active consumers in that PR and cleans the corresponding compatibility entries, recording the allowlist count at each step and which PR removes the last pair. Canonical injection behavior remains covered; frozen historical evidence bytes are not edited.
• R2 eliminates the six modules' infra/model reachability with positive/negative and platform-sensitive checks, covering both the package-level inferrsi.infra and inferrsi.infra.artifacts edges, not a permanent allowance for Harness-to-infra imports, and keeping Harness -> model at zero.
• R3 resolves the actual five reviewed execution-loader boundaries. Do not merely remove declarations, relax scanners or change expected output to manufacture isolation.
• On the final exact tree: first_wave_report().blockers == (), new_core_closure_isolated is True, and isolation_complete is True. Harness has zero edges into inferrsi.infra or inferrsi.model; the permanent neutral-leaf importer rule from R1 is part of this gate and is not counted as a compatibility pair. Negative controls reject old core paths, hidden dynamic imports and temporary forwarding.
• The tracked root-file set is exactly {__init__.py, __main__.py}; wheel checks separately allow only the declared generated _version.py metadata. Installed-wheel/resources/host and Windows/Linux checks pass without changing original byte/fact/security contracts.
• Record all retired paths and replacements in CHANGELOG. Root physical cleanliness and dependency isolation are both required; neither substitutes for the other.

Delivery discipline

• One implementation Claude session handles only the current PR in an isolated worktree. A second Claude session may only plan the next PR in a separate planning worktree; it must not edit source.
• Move implementation, update all active consumers/docs/tests, and delete the corresponding old root modules in the same PR. Do not introduce permanent compatibility shells or module-registry aliases.
• Preserve CLI command behavior, original evidence bytes, record/format contracts and isolation/security checks. Announce retired Python import/serialization module paths; historical frozen evidence remains pinned to its original commit or wheel, not rewritten.
• Before each implementation or review handoff, refresh main and confirmed dependencies. A completed plan is not implementation or approval. No automatic merge.

Historical context retained

The 2026-11-12 R01 scope already required retirement of seven Knowledge shells, three B01 root forwarders, the legacy manifest/allowlist and affected protected roots; installed-wheel/host checks and real positive/negative closure remained mandatory. Its final dependency list included K01/H02/B01/S01/OBS/A-entry, with no mandatory tag wait. The earlier permanent root CLI-forwarder carve-out and the assumption that every retirement must wait for the final PR are superseded by the owner's revised delivery decision. The neutral resource leaf still requires an explicitly reviewed no-core-import rule at its new canonical location; infra must not become a fourth core. No new product feature, K02 resource re-migration or formal replay/model experiment is included. Earlier issue discussion is retained; this update does not claim any new review or implementation acceptance.