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Two-phase Knowledge Refresh workflow (Phase A — Check drift [read-only] and Phase B — Refresh knowledge [scoped write]) with incremental, scoped, and full scopes and a 7-phase refresh pipeline (Detect -> Plan -> Investigate -> Reconcile -> Update -> Validate -> Commit Checkpoint).
Schema v2 for .codeintel/manifests/analysis_state.json with artifact-level depends_on tracking, structured claims[], staleness status (current, stale, unverified, deprecated), working-tree dirtiness flags, and in-place Schema v1 -> v2 migration.
Optional, controlled specialist subagent layer (skills/codeintel/agents/): 6 read-only role definitions (repository-mapper, behavior-tracer, change-impact-analyst, test-quality-analyst, defect-consistency-auditor, and knowledge-reconciler) with a single controlled Knowledge Writer.
Workflow Grounding (Consumer) mode and Before -> During -> After workflow lifecycle hook in SKILL.md, plus a Workflow & Subagent Context Pack handoff table in quick-start-template.md and task-routing-template.md so planning, implementation, TDD, debugging, and code-review workflows automatically discover and use .codeintel/.
Shared evidence model (skills/codeintel/references/evidence-model.md) and two-tier impact propagation guide (skills/codeintel/references/impact-analysis.md).
Schema templates in skills/codeintel/templates/: analysis-state-template.json, agent-result-template.json, and claim-template.json.
scripts/codeintel-refresh.sh for manifest/claim/agent-result validation, v1 -> v2 migration, drift detection, invalidation mapping, and atomic checkpoint updates.
tests/test-refresh.sh covering 11 fixture-based refresh and evidence validation scenarios in CI.