Enhance impact diagnostics and improve CLI documentation

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[Copilot]

Pull request overview

This PR extends Kibi’s “impact diagnostics / audit-quality diagnostics” surface area across the CLI, MCP server, and editor adapters (OpenCode, Cursor, Codex), while also updating documentation, tests, and package versions to match the new contracts.

Changes:

• Add/propagate impact-enabled kb_check guidance and tracking (including follow-up messages) in OpenCode/Cursor/Codex integrations.
• Introduce/standardize “advisory quality diagnostics” alongside existing hard violations, plus new/updated validation rules and richer typed fields (e.g., test verification metadata).
• Improve sync/status behavior around documentation README.md files and update docs/test entities to reflect the new behaviors.

Reviewed changes

Copilot reviewed 171 out of 172 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
packages/vscode/package.json	Bump extension version/deps (kibi-cli) and reformat metadata arrays.
packages/vscode/CHANGELOG.md	Add 0.4.7 entry for dependency updates.
packages/opencode/tests/smart-enforcement-policy.test.ts	Update assertions for new advisory guidance text.
packages/opencode/tests/prompt.coverage.test.ts	Add coverage for degraded-mode/cache/impact guidance behaviors.
packages/opencode/tests/file-operation-reminders.test.ts	Update reminder expectations; add test for impact-enabled kb_check guidance.
packages/opencode/src/scheduler.ts	Run kibi check in JSON mode and surface advisory quality diagnostics in logs.
packages/opencode/src/enforcement-policy.ts	Emit impact-enabled kb_check(...) guidance for edited source files.
packages/opencode/README.md	Document impact-enabled completion reminders and semantic-review intent.
packages/opencode/package.json	Bump version and kibi-cli dependency; reformat files list.
packages/opencode/CHANGELOG.md	Document advisory diagnostics surfacing + dependency bumps.
packages/mcp/tsconfig.json	Add path alias for public impact diagnostics types.
packages/mcp/tests/tools/validate-upsert.test.ts	Add integration preflight coverage for relationship validation.
packages/mcp/tests/tools/upsert.test.ts	Extend upsert tests for new metadata fields and improved errors.
packages/mcp/tests/tools/skills.test.ts	Assert declared skill resources are reported and hinted on errors.
packages/mcp/tests/tools/relationship-validation.test.ts	New test for actionable invalid-relationship formatting.
packages/mcp/tests/tools/find-gaps.test.ts	Add timeouts / formatting tweaks for integration stability.
packages/mcp/tests/tools/coverage.test.ts	Assert new coverage-depth fields and typed verification behavior.
packages/mcp/tests/tools/check-error-paths.test.ts	Update expectations for aggregated checks query behavior.
packages/mcp/tests/tools/check-aggregated-defaults.test.ts	New tests ensuring strict rules stay off by default.
packages/mcp/tests/tools/check-aggregated-config.test.ts	New tests ensuring explicit rule opt-in overrides config disables.
packages/mcp/tests/server/tools-coverage.test.ts	Align tool runtime signatures and ensure validate-upsert is invoked with prolog.
packages/mcp/tests/semantic-advisor/prose-coverage-fixture.ts	Add new corpus items for strict/predicate suggestions.
packages/mcp/tests/semantic-advisor/analyze-prose.test.ts	Add coverage for non-req payload and “already modeled” behavior.
packages/mcp/tests/diagnostics-helpers.test.ts	Add deterministic hinting for contradiction failures.
packages/mcp/tests/diagnostics-core.test.ts	Classify contradiction errors + extract semantic fields in diagnostics.
packages/mcp/src/tools/validate-upsert.ts	Add optional live relationship preflight (when invoked via MCP/prolog).
packages/mcp/src/tools/upsert.ts	Add live relationship target validation + improved error formatting + metadata fields.
packages/mcp/src/tools/skills.ts	Include declared resources in load output and hint on missing-resource errors.
packages/mcp/src/tools/query-plan-safety.ts	New helper to detect unsafe Prolog negation/generator ordering.
packages/mcp/src/tools/check-types.ts	New shared types for check args/results incl. quality/impact diagnostics.
packages/mcp/src/tools/check-prolog.ts	New aggregated Prolog check runner with allowlisting.
packages/mcp/src/tools/check-impact.ts	New bridge for impact diagnostics analysis in MCP check flows.
packages/mcp/src/tools/check-format.ts	New formatting/structured-content builder for violations/quality/impact output.
packages/mcp/src/tools/check-config.ts	New .kb/config.json loader + effective rule resolution for MCP checks.
packages/mcp/src/tools-config.ts	Expand kb_check schema/docs to cover impact options + new rules.
packages/mcp/src/server/tool-types.ts	Update runtime signature for kb_validate_upsert.
packages/mcp/src/server/tool-registration.ts	Ensure kb_validate_upsert is invoked with an ensured prolog instance.
packages/mcp/src/server/docs.ts	Update docs to distinguish targeted vs final unfiltered kb_check.
packages/mcp/src/semantic-advisor/prose-coverage-evaluator.ts	Extend prose coverage case schema with optional source.
packages/mcp/src/semantic-advisor/analyze-prose.ts	Add new strict-property and predicate detections (decisecond slot, merge policy).
packages/mcp/src/diagnostics-helpers.ts	Classify semantic contradictions and add actionable hints/id extraction.
packages/mcp/package.json	Bump version and update kibi-cli/kibi-core dependencies.
packages/mcp/CHANGELOG.md	Document coverage depth + quality diagnostics contract + rule additions.
packages/cursor/tests/messages.test.ts	Update stop follow-up behavior tests for impact-enabled guidance.
packages/cursor/tests/hook-runner.test.ts	Add stop-follow-up scenarios for missing vs completed impact checks.
packages/cursor/src/path-policy.ts	Treat .pl as source; add source-impact relevance predicate.
packages/cursor/src/messages.ts	Emit impact-check follow-up messaging for source edits.
packages/cursor/src/kb-mcp-tools.ts	Parse kb_check calls and detect impact-enabled runs + affected sourceFiles.
packages/cursor/src/hook-state.ts	Track impact-check completion + paths in persisted hook state.
packages/cursor/src/hook-runner.ts	Record parsed MCP tool calls (including impact-check metadata).
packages/cursor/src/guidance.ts	Add explicit impact-enabled kb_check line in write guidance.
packages/cursor/skills/kibi-usage/SKILL.md	Update skill guidance for qualityDiagnostics + impact-enabled kb_check workflows.
packages/cursor/skills/kibi-traceability/SKILL.md	Add impact-check step and semantic-review interpretation guidance.
packages/cursor/rules/kibi-traceability.mdc	Add impact-check step to traceability rule.
packages/cursor/README.md	Update behavior description to include impact-check follow-up.
packages/cursor/package.json	Bump package version.
packages/cursor/CHANGELOG.md	Document quality diagnostics support in Cursor adapter.
packages/cursor/.cursor-plugin/plugin.json	Bump plugin version.
packages/core/src/status.pl	Ignore documentation README files in freshness checks.
packages/core/schema/entities.pl	Add typed symbol metadata + typed test verification fields to schema.
packages/core/package.json	Bump version and reformat files list.
packages/core/CHANGELOG.md	Document coverage depth, diagnostics, and README ignore behavior.
packages/codex/tests/hook-state.test.ts	Update empty-state expectations to include impact-check state.
packages/codex/tests/hook-runner.test.ts	Add stop-follow-up tests for missing vs completed impact checks.
packages/codex/src/path-policy.ts	Treat .pl as source; add source-impact relevance predicate.
packages/codex/src/messages.ts	Add impact-check reminder message builder.
packages/codex/src/kb-mcp-tools.ts	New: parse kb_check calls and detect impact-enabled runs + sourceFiles.
packages/codex/src/hook-runner.ts	Record MCP tool calls and emit impact/freshness reminders on stop.
packages/codex/skills/kibi-usage/SKILL.md	Update skill guidance for qualityDiagnostics + impact-enabled kb_check workflows.
packages/codex/skills/kibi-traceability/SKILL.md	Add impact-check step and semantic-review interpretation guidance.
packages/codex/package.json	Bump package version.
packages/codex/CHANGELOG.md	Document quality diagnostics support in Codex adapter.
packages/codex/.codex-plugin/plugin.json	Bump plugin version.
packages/cli/tests/utils/rule-registry.test.ts	Add tests for new rule registry entries and enablement defaults.
packages/cli/tests/utils/prolog-query-plan-safety.test.ts	New tests for Prolog query plan safety analyzer.
packages/cli/tests/traceability/symbol-extract.test.ts	Add coverage for class property/accessor symbol extraction.
packages/cli/tests/traceability/staged-symbols-manifest.test.ts	Add evidence collection for changed authored manifest entries.
packages/cli/tests/traceability/staged-impact-contract.test.ts	Update staged diagnostics contract for docs/suggestions/blocking semantics.
packages/cli/tests/traceability/impact-symbol-quality-fixtures.ts	New fixtures for symbol quality diagnostics tests.
packages/cli/tests/traceability/impact-symbol-mixed-purpose.test.ts	New tests for mixed-purpose symbol review diagnostics.
packages/cli/tests/traceability/evidence-model.test.ts	Update staged evidence diagnostics to include blocking/category and new docs link.
packages/cli/tests/skills-content.test.ts	Update skill content expectations and add coverage for new guidance sections.
packages/cli/tests/extractors/symbols-ts.test.ts	Add coordinate enrichment fallback coverage for class members.
packages/cli/tests/commands/sync/discovery.test.ts	Assert README ignore behavior in markdown discovery.
packages/cli/tests/commands/sync.test.ts	Improve sync error context assertions (source/fact_kind/value field).
packages/cli/tests/commands/status.test.ts	Add regression test for README ignore keeping status fresh.
packages/cli/tests/commands/coverage.test.ts	Assert coverage-depth fields and ensure table renders depth labels.
packages/cli/tests/commands/check-staged-enforcement.test.ts	Add tests for advisory quality diagnostics printing without failing.
packages/cli/tests/commands/check-impact-contract.test.ts	Add tests for blocking vs advisory quality diagnostics semantics.
packages/cli/src/utils/rule-registry.ts	Register new rules (predicate-verifiability, query-plan-safety).
packages/cli/src/utils/prolog-query-plan-safety.ts	New analyzer for unsafe negation/generator ordering in Prolog clauses.
packages/cli/src/types/entities.ts	Add typed test verification metadata to TestEntity.
packages/cli/src/traceability/symbol-extract.ts	Extract class properties/accessors as member symbols for impact/traceability.
packages/cli/src/traceability/staged-symbols-manifest.ts	Only report authored symbol IDs whose staged metadata actually changed.
packages/cli/src/traceability/staged-impact-contract.ts	Clarify staged evidence guidance (MCP writes don’t stage artifacts).
packages/cli/src/traceability/staged-diagnostics.ts	Expand diagnostics to QualityDiagnostic shape with blocking/category/docs updates.
packages/cli/src/traceability/evidence-model.ts	Add dedicated staged-impact docs anchor constant.
packages/cli/src/public/symbol-granularity.ts	Treat property/accessor as behavioral symbol kinds.
packages/cli/src/public/skills/kibi-usage/SKILL.md	Update examples to supported typed values + add “Small Behavior Fix” recipe.
packages/cli/src/public/skills/kibi-usage/resources/workflows.md	Add workflow for behavior fixes without existing requirements.
packages/cli/src/public/skills/kibi-usage/resources/relationship-directions.md	Add explicit “invalid test-fact shortcut” guidance.
packages/cli/src/public/skills/kibi-usage/resources/fact-lanes.md	Clarify strict fact schema value types and update examples.
packages/cli/src/public/schemas/entity.ts	Allow typed test verification fields only for type: test entities.
packages/cli/src/public/impact/types.ts	New: public impact/quality diagnostic types.
packages/cli/src/public/impact/summaries.ts	New: summarize extracted symbols, linked entities, and next actions.
packages/cli/src/public/impact/manifest.ts	New: read/normalize manifest results for impact analysis.
packages/cli/src/public/impact/analyzer.ts	New: compute changed-file impact diagnostics from staged/working tree inputs.
packages/cli/src/public/impact-diagnostics.ts	New: public entrypoint exports for impact diagnostics.
packages/cli/src/extractors/symbols-ts.ts	Include class properties/accessors in TS symbol extraction + coordinate lookup.
packages/cli/src/extractors/symbols-coordinator.ts	Add property/accessor symbol kinds to coordinator contract.
packages/cli/src/extractors/markdown.ts	Extend extracted entity shape to include symbol coordinate/kind/role fields.
packages/cli/src/extractors/manifest.ts	Pass through additional symbol metadata fields from manifest records.
packages/cli/src/commands/sync/persistence.ts	Persist typed test verification fields; enrich error context with semantic details.
packages/cli/src/commands/sync/discovery.ts	Ignore **/README.md during markdown discovery and filter residual README paths.
packages/cli/src/cli.ts	Add `--format text
packages/cli/schema/entities.pl	Add typed symbol metadata fields to CLI schema copy.
packages/cli/package.json	Bump version, add public impact-diagnostics export, update deps, reformat files list.
documentation/tests/TEST-opencode-advisory-diagnostics.md	New KB test entity documenting OpenCode advisory diagnostics coverage.
documentation/tests/TEST-mcp-quality-diagnostics-contract.md	New KB test entity documenting MCP quality diagnostics contract coverage.
documentation/tests/TEST-coverage-depth-labels.md	New KB test entity for coverage-depth labels/diagnostics.
documentation/tests/TEST-cli-sync-discovery-readme-ignore.md	New KB test entity for README ignore regression.
documentation/tests/TEST-cli-symbol-quality-diagnostics.md	New KB test entity for CLI symbol quality diagnostics coverage.
documentation/tests/TEST-cli-status-pre-first-sync.md	Expand description to include README ignore freshness behavior.
documentation/tests/TEST-cli-requirement-quality-diagnostics.md	New KB test entity for requirement quality diagnostics coverage.
documentation/tests/TEST-cli-quality-diagnostics-contract.md	New KB test entity for CLI quality diagnostics contract coverage.
documentation/tests/TEST-cli-mixed-purpose-diagnostics.md	New KB test entity for mixed-purpose symbol diagnostics coverage.
documentation/tests/TEST-audit-quality-diagnostics-v1.md	New rollup test entity for audit-quality diagnostics scenario.
documentation/tests/TEST-002.md	Fix link type (change specifies to validates).
documentation/tests/e2e/packed/fixtures/README.md	Add frontmatter (but README is now treated specially by discovery/freshness).
documentation/scenarios/SCEN-release-automation.md	Remove incorrect/unused specified_by link block.
documentation/scenarios/SCEN-audit-quality-diagnostics-v1.md	New scenario defining the two-lane diagnostics behavior.
documentation/scenarios/SCEN-001.md	Remove validates links (leaving verified_by links).
documentation/requirements/REQ-audit-quality-diagnostics-v1.md	New requirement describing two-lane diagnostics contract across surfaces.
docs/symbol-traceability-taxonomy.md	Document member-level behavioral anchors + semantic review after source edits + audit diagnostics lane.
docs/prompts/llm-rules.md	Update guidance on targeted vs final unfiltered kb_check.
docs/modeling-cheatsheet.md	Add guidance on small behavior fixes and qualityDiagnostics lane semantics.
docs/error-reference.md	Document invalid relationship tuples + advisory diagnostics lane semantics.
docs/entity-schema.md	Document coverageDepth labels and two-lane check output contract; clarify fact/test relationship shapes.
AGENTS.md	Update non-negotiables to allow CLI-only workflows when MCP has no equivalent; strengthen freshness handoff requirement.
.cursor/rules/kibi-traceability.mdc	Mirror impact-check guidance in root Cursor ruleset.