Layer the Tool runtime by Area and Domain, and retire the legacy interface closure

[KimGLee]

Owner Issue

Closes #179

Problem

The Tool layer had accumulated every responsibility in one flat Tools/ namespace. Governance control, task execution, knowledge production, and platform interfacing were interleaved with the CLI entry points that expose them, so no module had an exclusive owner, implementations were duplicated, dependency direction was unstated, legacy compatibility interfaces could not retire, and tests were organized against historical file locations rather than owned contracts.

The confirmed Tool taxonomy declared Areas and Domains that had no physical counterpart on disk. This PR makes that taxonomy the physical structure.

It is intentionally one atomic change. Moving modules without moving their entry points, imports, capability registrations, interface policy, distribution boundary, catalogs, tests, and generated projections would leave the repository unable to satisfy its own boundary checks.

Changes

Physical Area/Domain layering

Every Tool module now has exactly one Area and Domain, expressed as its location on disk:

Area	Domains	Modules
Tools/governance/	standards, profile, control	15
Tools/execution/	task_runtime, planning, context_delivery, evidence, audit	103
Tools/knowledge/	content, metadata, structure, rendering	29
Tools/platform/	agent_interface, distribution, repository, common	27

Tools/queue_runtime/ moved under its owner as Tools/execution/task_runtime/queue_runtime/.

Public entry surface closed

• The top level of Tools/ now holds 63 registered entry points only — thin CLI commands, mcp_server.py, and the catalog generators.
• Every entry is 19–50 lines (average 21) and does nothing but delegate to its owning Domain. No entry point holds logic, and none is importable as a library.
• Baseline was 105 top-level modules mixing entries and implementations; the implementation is now 174 modules under the four Areas.

Contracts, registration, and boundaries realigned

• Rewrote imports across the tree to the new physical paths, with import direction now explicit and checkable against the layering.
• Updated capability registration (operation-capabilities.yaml, scan-capabilities.yaml), agent interface policy (agent-interface-policy.yaml), module boundaries (module-boundaries.yaml), test ownership (test-ownership.yaml), and the distribution boundary (distribution-boundary.yaml) to describe the layout that actually exists.
• Updated Tools/README.md, the root README.md / README.zh-CN.md, ROADMAP.md / ROADMAP.zh-CN.md, the affected Cards, and the Kernel standards under K00, K02, K06, K08, K12, and K13.

Test system returned to its owning layer

• Reorganized tests by the layer that owns the contract under test — 127 test modules.
• Tools/TEST_CATALOG.md and Tools/TOOL_CATALOG.md attribute every tool and every test to its owning Area/Domain, so an unowned or orphaned test is detectable rather than invisible.
• Bound Runner dispatch to the Tool contracts each tool actually carries, rather than to a name-based lookup.

Retired interfaces

Removed rather than kept reachable as a second authority:

Retired	Kind
Tools/queue_runtime/producer_era.py	producer-era compatibility shim
Tools/queue_runtime/__init__.py	package-level compatibility re-export surface
Tools/migrate_standards_state.py	migration bridge
Tools/schemas/component-path-migrations.yaml	component-path migration bridge
Tools/apply_task_plan.py	superseded implementation
Tools/batch_close_contract.py	superseded implementation
Tools/coverage_contract.py, Tools/coverage_delta.py	superseded implementations
Tools/audit_evidence_runtime.py	superseded implementation
Tools/module_boundary_facts.py	superseded implementation
Tools/queue_runtime/review.py	superseded implementation

Their tests were retired with them (test_migrate_standards_state.py, test_reviewed_era_lifecycle.py, test_corpus_plan_bootstrap.py, test_json_flag_verdict_parity.py, test_stamp_cards_skeleton.py, test_template_fill.py). Old internal paths are not retained as aliases.

The last two commits close the contract gaps this exposed: planning and terminal evidence contracts, and Runner dispatch binding to carried Tool contracts.

Generated projections

Rebuilt from their canonical owners, and failing when their source contracts drift:

• Tools/compiled/cli-contract.yaml
• Tools/compiled/mcp-tools.json
• Tools/compiled/metadata-execution-contract.json
• Tools/compiled/tool-catalog.json
• Tools/compiled/test-catalog.json
• Tools/compiled/host-configs/

Validation

• make check passes.
• Catalog full test run: 1079/1079 tests, 127/127 modules pass.
• Required Queue E2E passes.
• Blank runtime lifecycle exercised end to end.
• Atlas dynamic acceptance: hard cutover onto Cambium 321b530d6ccc86f1ac3d3a5a7214043594e3a929, dynamic batch close completed.
  • Atlas B001 = closed
  • runtime errors = 0
  • AuditPlan 51/51 obligations closed
  • unresolved = 0

Follow-up: host-independent runner contract (990d817)

The first CI run failed verify check: the runner's --python argument defaulted to sys.executable, freezing the generating machine's absolute interpreter path into Tools/compiled/cli-contract.yaml, so the projection could never verify as current on another host. 990d817 declares the default as None, resolves the current interpreter at dispatch time, and rebinds the interface and host-config projections. make check and the full catalog run (1079/1079, 127/127) pass against the corrected contract.