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Phase 3: Status Reclassification -- All Changes reference

Note: All 49 PARTIALLYIMPLEMENTED gaps from the audit map to INPROGRESS. All 29 NOTSTARTED gaps from the audit become either OPEN (22) or NEEDSRESPEC (7, where the spec's architectural assumptions are outdated).

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Gap Status Matrix Genty Stack Roadmap Next Steps Gap Inventory: Category Summary Phase 1 Inventory Adversarial Check Results Phase 2 Codebase Audit -- Adversarial Corrections Phase 2: Stale Paths Report Phase 3: Closed Gaps Phase 4: Critical Path Analysis Phase 4: Parallel Work Tracks Phase 5: Quick Wins Phase 5: Risk Register Phase 6: Milestone Summary Phase 6: Roadmap

Phase 3: Status Reclassification -- All Changes

Summary

Final Status	Count
CLOSED	69
IN_PROGRESS	49
OPEN	22
NEEDS_RESPEC	7
OBSOLETE	0
BLOCKED	0

**Total: 147 gaps**

Note: All 49 PARTIALLY_IMPLEMENTED gaps from the audit map to IN_PROGRESS. All 29 NOT_STARTED gaps from the audit become either OPEN (22) or NEEDS_RESPEC (7, where the spec's architectural assumptions are outdated).

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Status Changes from Original Inventory

The table below lists every gap where the final status differs from the original Phase 1 inventory status. Gaps that remained unchanged (original Partial -> IN_PROGRESS, original Missing -> OPEN) are included only when the assessment has materially changed.

Gaps Upgraded to CLOSED (69 total)

These gaps are fully implemented and meet their target state.

Gap ID	Title	Original Status	Final Status	Reason
GAP-AGENT-007	Delegation Policy Layer	Missing	CLOSED	Full governance engine with policy engine, categories (A/B/C/D), sandbox policy, posture bridge. SDK PolicyRule types cover all required rule types.
GAP-AGENT-008	Harness Selection Policies	Missing	CLOSED	selectionPolicies.ts provides 4 named policies. capabilityRouter.ts provides selectHarness with scoring against task requirements.
GAP-BRK-001	Breakpoint Approval Chains and Escalation	Missing	CLOSED	approvalChains.ts provides multi-stage chains with ApprovalChainStep, QuorumConfig, and timeout-based escalation.
GAP-BRK-002	Breakpoint Delegation to External Systems	Missing	CLOSED	delegation.ts provides webhook-based routing with DelegationRule, full async approval workflow with timeouts and retries.
GAP-HADAPT-001	Capability-Based Task Routing	Partial	CLOSED	capabilityRouter.ts with buildTaskRequirements()/selectHarness(), HarnessCapability enum on all adapters, TaskRequirements fully defined.
GAP-HADAPT-002	Model Selection Per Task	Missing	CLOSED	modelSelection.ts bridges task-level model preferences with harness capability routing.
GAP-HADAPT-004	Harness Fallback Chains	Missing	CLOSED	fallbackChains.ts provides FallbackChain, FallbackResolution, chain creation, and exhaustion detection.
GAP-JSON-001	JSON API for Run Creation and Management	Partial	CLOSED	Full API in api/runs.ts with ApiResult envelopes. MCP tools expose run_create, run_iterate, run_status.
GAP-JSON-002	JSON Effect Dispatch and Response Protocol	Missing	CLOSED	Full typed API in api/effects.ts with listing, showing, cancelling, and batch-committing.
GAP-JSON-003	JSON Breakpoint Interaction API	Missing	CLOSED	Full JSON API in api/breakpoints.ts for listing, context, approval/rejection with feedback.
GAP-JSON-005	JSON Event Stream (SSE/WebSocket)	Missing	CLOSED	eventStream.ts subscription management, journalWatcher.ts real-time streaming, WebSocket transport.
GAP-MCPC-001	MCP Channel Integration (Inbound Messaging)	Missing	CLOSED	Full channel manager, InboundMessageQueue with WakeCallback, channel allowlist, capability detection.
GAP-MCPC-002	MCP Channel Outbound Messaging	Missing	CLOSED	OutboundChannelSender with template messaging, DEFAULT_CHANNEL_TOOL_MAPPINGS for Slack/Discord/email.
GAP-MCPC-004	MCP Server Management UI and Connection Lifecycle	Missing	CLOSED	McpClientManager with full connect/disconnect lifecycle, status tracking, reconnection, tool registry.
GAP-OBS-001	Run Health Snapshot	Partial	CLOSED	computeRunHealthFromEvents with RunHealthSnapshot, configurable thresholds, stuck/error/pending detection.
GAP-OBS-002	Phase Timeline Visualization	Partial	CLOSED	timeline.ts synthesizes PhaseTimeline with phase entries, durations, iteration timeline, and milestones.
GAP-OBS-004	Policy Decision Trail	Missing	CLOSED	DecisionTrailEntry/PolicyEvalRecord for audit trail. governance-decisions.jsonl for persistent logging.
GAP-OBS-NEW-002	Dashboard API for External Dashboards	Missing	CLOSED	Full API layer in api/ (runs, effects, breakpoints, event streams). MCP tools expose as JSON.
GAP-PAR-002	Async Effect Execution	Missing	CLOSED	asyncEffects.ts classifies blocking/background. BackgroundEffectEntry/BackgroundProcessRegistry.
GAP-PAR-009	Parallel Effect Execution Strategies	Partial	CLOSED	4 named strategies (all-or-nothing, best-effort, first-success, quorum). Execution wave building.
GAP-PERF-005	Cache-Aware Prompt Assembly	Missing	CLOSED	PART_STRATA_MAP with volatility scores, STRATUM_ORDER stable-first, composeByStrataWithMeta with checksums.
GAP-PERF-006	Incremental Orchestration Streaming	Missing	CLOSED	JournalWatcher real-time streaming, eventStream.ts subscriptions, WebSocket transport.
GAP-PERF-008	Structured Continuity State	Partial	CLOSED	continuityState.ts with ContinuityPhase, key decisions, working files, findings. Persists across compaction.
GAP-PROC-002	Process Nesting and Sub-Process Invocation	Missing	CLOSED	Full ctx.subprocess() in subprocess.ts with SubprocessInvocation type including all required fields.
GAP-PROC-004	Process Parameter Schemas and Validation	Missing	CLOSED	schemaValidator.ts validates JSON Schema (draft-07 subset). SubprocessInvocation has inputSchema/outputSchema.
GAP-PROMPT-001	Prompt Strata Model	Partial	CLOSED	Complete strata model in strata.ts: STRATUM_ORDER, PART_STRATA_MAP (30+ parts), composeByStrataWithMeta.
GAP-PROMPT-002	Deterministic Capability Projection	Partial	CLOSED	capabilityCollector.ts queries all surfaces, produces sorted deterministic capability arrays.
GAP-PROMPT-003	Runtime Personality Overlays	Partial	CLOSED	modeSelector.ts provides 4 modes (interactive, autonomous, plan, fast) with per-mode configuration.
GAP-PROMPT-005	Continuity Overlays for Resume	Partial	CLOSED	continuityOverlay.ts builds from journal/artifacts/history. Renders into prompts with effects, decisions, files.
GAP-PROMPT-008	Coding Philosophy Prompt Section	Missing	CLOSED	codingPhilosophy.ts with render function, coding-philosophy.md template, mapped in PART_STRATA_MAP.
GAP-PROMPT-009	Tool Preference and Usage Rules	Missing	CLOSED	toolPreferences.ts with render function, tool-preferences.md template, mapped in PART_STRATA_MAP.
GAP-PROMPT-011	Output Efficiency Rules	Missing	CLOSED	outputEfficiency.ts with render function, output-efficiency.md template, mapped in PART_STRATA_MAP.
GAP-PROMPT-012	Git Safety Protocol Prompt Section	Missing	CLOSED	gitSafety.ts with render function, git-safety.md template, mapped in PART_STRATA_MAP.
GAP-REMOTE-001	Daemon Mode	Partial	CLOSED	Full daemon with lifecycle, event loop, file watcher, cron scheduler, webhook listener, durable queue.
GAP-REMOTE-004	Cron Triggers and Scheduling	Missing	CLOSED	timerScheduler.ts with parseCron, macros, timezone support. Integrated into daemon loop.
GAP-REMOTE-006	MCP Client Integration	Partial	CLOSED	Full MCP client with manager, config, toolRegistry, executor. Pluggable transport.
GAP-REMOTE-008	Streaming Orchestration Protocol	Missing	CLOSED	JournalWatcher + eventStream.ts + WebSocket transport for real-time event delivery.
GAP-REMOTE-009	Host-Mediated Interaction	Partial	CLOSED	breakpoints.ts API with context/options, permissionRelay.ts, HostContract interface.
GAP-ROUTE-001	Smart Effect Routing Engine	Missing	CLOSED	capabilityRouter.ts full routing, selectionPolicies.ts policy evaluation, modelSelection.ts bridge.
GAP-SEC-001	Governance Policy Layer	Missing	CLOSED	Full engine with createPolicyEngine(), deny>warn>allow precedence, PolicyRule types, JSONL logging, tiers.
GAP-SEC-003	Permission Request and Denial Hooks	Partial	CLOSED	InteractionKind with 5 types, interactionRouter.ts UX mapping, on-permission-denied hook.
GAP-SEC-004	Sandbox Toggle	Partial	CLOSED	SandboxPolicy with rules/defaultAction, sandboxBridge.ts governance integration, piSecureSandbox.ts Docker.
GAP-SEC-005	Approval Posture Model	Partial	CLOSED	DEFAULT_POSTURES per ActionCategory, postureBridge.ts converts to PolicyRule[].
GAP-SESSION-001	Session-to-Run One-to-Many	Missing	CLOSED	SessionContext with cross-run knowledge, SessionRunSummary array, SessionState.runIds.
GAP-SESSION-002	Session State Persistence and History	Missing	CLOSED	SessionHistory with decisions/summaries/snapshots. persistence.ts with findings/modifications/patterns.
GAP-SESSION-004	Session-Level Cost Tracking	Missing	CLOSED	SessionBudget, SessionCostSummary, budget threshold alerts, atomic persistence.
GAP-STATE-003	Session State Persistence	Partial	CLOSED	persistence.ts stores SessionFinding, file modifications, breakpoint patterns, preferences.
GAP-STATE-008	Run Health Model	Missing	CLOSED	computeRunHealthFromEvents with thresholds, RunHealthSnapshot, stuck/error/noop detection.
GAP-SUBOBS-003	Per-Subagent Token and Cost Tracking	Missing	CLOSED	EffectCostSummary per-effect breakdown. Full pricing tables and journal cost collection.
GAP-TOOLS-008	Web Search Agentic Tool	Missing	CLOSED	web_search tool with query, max_results, domains, exclude_domains. HTML extraction.
GAP-TOOLS-014	Programmatic Task CRUD	Partial	CLOSED	tasks/crud.ts full CRUD. api/effects.ts effect API. MCP task_list/show/cancel/post.
GAP-TOOLS-018	Structured Planning Phase	Partial	CLOSED	planMode.ts with PlanStep, status, dependencies, verification, approval, modification.
GAP-TOOLS-020	Scheduled Orchestration Triggers	Missing	CLOSED	Full daemon scheduling: timerScheduler.ts, automationExecutor.ts, daemon loop integration.
GAP-TOOLS-021	External Event Triggers	Missing	CLOSED	webhookListener.ts HTTP, fileWatcher.ts filesystem, automationExecutor.ts event-to-process mapping.
GAP-TOOLS-025	MCP Tool Discovery and Invocation	Partial	CLOSED	Full MCP client with toolRegistry, executor, manager. tool_search and tool_fetch agentic tools.
GAP-TOOLS-027	Skill Discovery and Invocation	Partial	CLOSED	SkillRouter, SkillDiscoveryService, SkillChainBuilder, skill_discover MCP tool.
GAP-TOOLS-030	Effect Cancellation	Missing	CLOSED	commitEffectCancellation(), EffectCancelledError, task_cancel CLI/MCP, processControl SIGTERM/SIGKILL.
GAP-TOOLS-033	Runtime Configuration Tool	Missing	CLOSED	config agentic tool with get/set/list/reset. Run-scoped entries. Model/compression/breakpoint support.
GAP-TOOLS-034	Dynamic Tool Discovery and Search	Missing	CLOSED	deferredToolRegistry.ts two-tier index, tool_search/tool_fetch agentic tools, ToolSource categories.
GAP-TOOLS-035	Grep Output Modes and Context Params	Missing	CLOSED	grep tool with output_mode, before_context, after_context, line_numbers, head_limit, offset, multiline.
GAP-TOOLS-036	Bash Background Execution	Missing	CLOSED	bash tool with run_in_background, description, BackgroundProcessRegistry, background_status tool.
GAP-TOOLS-038	Ask Tool Interaction Model Alignment	Missing	CLOSED	AskUserQuestion with mode param: simple (CC-compatible) and structured (babysitter).
GAP-USER-001	Operator Command Layer	Partial	CLOSED	operatorCommands.ts with categories, commandTemplate, breakpoint integration.
GAP-USER-006	Real-Time Cost Tracking	Partial	CLOSED	effectCost.ts per-effect, pricing.ts tables, session/cost.ts budgets with auto-pause.
GAP-USER-012	Plan Mode with Verification	Partial	CLOSED	planMode.ts full plan mode with steps, status, dependencies, verification, approval.
GAP-UX-005	Structured Orchestration Status View	Partial	CLOSED	getOrchestrationStatus combining metadata, health, pending effects. JSON support.
GAP-UX-006	Pending Work Inspector	Partial	CLOSED	getPendingWorkItems, batching groups, getEffectiveConcurrency. JSON output.
GAP-UX-007	Rich Breakpoint Interaction	Partial	CLOSED	interactionRouter.ts UX hints, postures.ts risk resolution, operatorCommands.ts, API context.
GAP-UX-014	Operator Mode Selection	Partial	CLOSED	modeSelector.ts with 4 modes, getModeConfig/switchMode, per-mode config.

Gaps Upgraded to IN_PROGRESS (from Missing) (25 total)

These were originally marked as Missing but have partial implementations discovered during the codebase audit.

Gap ID	Title	Original Status	Final Status	Reason
GAP-AGENT-006	Cross-Run State Sharing	Missing	IN_PROGRESS	SessionContext and SessionHistory provide cross-run shared knowledge.
GAP-ECO-001	CC Plugin Compatibility Layer	Missing	IN_PROGRESS	Plugin loader, sandbox, version-check exist; CC manifest adapter missing.
GAP-ECO-003	Plugin Trust, Provenance, and Blocklist	Missing	IN_PROGRESS	Sandbox permissions and governance trust-level rules exist; blocklist/provenance missing.
GAP-ECO-004	Plugin Auto-Update and Versioning	Missing	IN_PROGRESS	Semver checks and registry exist; auto-update and rollback missing.
GAP-ECO-005	Plugin Validation and Diagnostics	Missing	IN_PROGRESS	Loader and version-check exist; validate command and structured errors missing.
GAP-HADAPT-003	Cost-Based Routing Policies	Missing	IN_PROGRESS	Cost-optimized policy, pricing tables, budget thresholds exist; auto-downgrade missing.
GAP-HADAPT-005	Harness Health Monitoring and Circuit Breaker	Missing	IN_PROGRESS	Run health scoring exists; per-harness monitoring and circuit breaker missing.
GAP-JSON-004	JSON Session Management API	Missing	IN_PROGRESS	MCP tools expose session ops; unified REST API missing.
GAP-MCPC-003	Channel Permission Relay	Missing	IN_PROGRESS	ChannelPermissionRelay with racing pattern exists; not wired into breakpoint flow.
GAP-OBS-NEW-001	Webhook and Alert System	Missing	IN_PROGRESS	Registration types and registry exist; HTTP delivery and integrations missing.
GAP-PERF-001	Prompt Caching (Ephemeral)	Missing	IN_PROGRESS	Strata-aware assembly with cache-break detection exists; API cache_control not wired.
GAP-PERF-004	Streaming Message Rendering	Missing	IN_PROGRESS	Pi streaming and JournalWatcher exist; CLI harness streaming and dashboard missing.
GAP-PROC-001	Process Chaining and Pipelines	Missing	IN_PROGRESS	SkillChainBuilder provides topological sorting and dependency tracking. Full process pipeline missing.
GAP-PROF-001	Auto-Configure from User Profile	Missing	IN_PROGRESS	Profile system renders to prompts; not used for orchestration auto-configuration.
GAP-PROMPT-006	Instructions Loaded Hook	Missing	IN_PROGRESS	Adapter-specific hook exists; not generalized to SDK-level.
GAP-PROMPT-010	Safety/Reversibility Prompt Framework	Missing	IN_PROGRESS	criticalRules.ts and nonNegotiables.ts exist; dedicated reversibility framework missing.
GAP-REMOTE-003	Remote Sessions (WebSocket)	Missing	IN_PROGRESS	WebSocket transport with multiplexing and auth exists; run directory sync missing.
GAP-REMOTE-007	Host Contract Layer	Missing	IN_PROGRESS	Types and validation in hostContract.ts; methods not implemented, zero consumers.
GAP-ROUTE-002	Effect Priority and Scheduling	Missing	IN_PROGRESS	Parallel strategies and scheduler hints exist; priority queue missing.
GAP-SEC-002	Trust Classes for Plugins	Missing	IN_PROGRESS	Sandbox permissions and governance rules exist; TrustLevel field missing.
GAP-STATE-001	Long-Term Memory Extraction	Missing	IN_PROGRESS	memoryExtraction.ts exists; memories not injected into prompts.
GAP-SUBOBS-001	Streaming Output Capture	Missing	IN_PROGRESS	Pi subscribe() works; CLI harness streaming missing.
GAP-SUBOBS-002	Subagent Progress Tracking	Missing	IN_PROGRESS	Background status tracking exists; percentage/ETA missing.
GAP-SUBOBS-004	Subagent Health and Timeout	Missing	IN_PROGRESS	Timeout tracking exists; health monitoring and auto-recovery missing.
GAP-TOOLS-031	MCP Resource Browsing and Reading	Missing	IN_PROGRESS	MCP client exists; agentic tools for resource browsing missing.

Gaps Reclassified to NEEDS_RESPEC (7 total)

These gaps reference architectural assumptions that are no longer valid.

Gap ID	Title	Original Status	Final Status	Reason
GAP-SUBOBS-005	Dashboard Subagent Drill-Down	Missing	NEEDS_RESPEC	Assumes 'embedded SDK dashboard' (packages/babysitter-sdk/src/dashboard/) which does not exist. Architecture has evolved to observer-dashboard and tula-ui.
GAP-UX-001	Ink/React Terminal Rendering Foundation	Missing	NEEDS_RESPEC	Assumes Ink-based components inside SDK. Architecture evolved to tula-ui extraction and observer-dashboard.
GAP-UX-001a	Effect Tree Visualization	Missing	NEEDS_RESPEC	Depends on GAP-UX-001's Ink assumption, which is outdated.
GAP-UX-001b	Structured Diff Rendering	Missing	NEEDS_RESPEC	Depends on GAP-UX-001's Ink assumption, which is outdated.
GAP-UX-001d	Message Type Rendering	Missing	NEEDS_RESPEC	Depends on GAP-UX-001's Ink assumption, which is outdated.
GAP-UX-001e	Progress and Status Line	Missing	NEEDS_RESPEC	Depends on GAP-UX-001's Ink assumption, which is outdated.
GAP-UX-001f	Streaming Output Panels	Missing	NEEDS_RESPEC	Depends on GAP-UX-001's Ink assumption, which is outdated.

Unchanged Status Gaps

The remaining gaps maintained their expected status mapping:

**24 IN_PROGRESS** gaps: Originally Partial that remained as partial implementations (mapped to IN_PROGRESS)
**22 OPEN** gaps: Originally Missing that remained NOT_STARTED (mapped to OPEN), with 7 additional NOT_STARTED gaps reclassified to NEEDS_RESPEC due to outdated architectural assumptions

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Priority Reclassification for Non-CLOSED Gaps

Critical Priority (2 gaps)

Gap ID	Title	Status	Original Priority	Remaining Effort
GAP-ECO-001	CC Plugin Compatibility Layer	IN_PROGRESS	Critical	L
GAP-PERF-002	Session Compaction	IN_PROGRESS	Critical	L

Note: GAP-PERF-001 (Prompt Caching) and GAP-SUBOBS-001 (Streaming Output Capture) were originally Critical and remain so.

Effort Reductions

Several IN_PROGRESS gaps have reduced remaining effort due to partial implementations:

GAP-HADAPT-003 (Cost-Based Routing): M -> S (only auto-downgrade wiring needed)
GAP-HADAPT-005 (Health Monitoring): M -> S (run health exists, need per-harness)
GAP-ECO-003 (Plugin Trust): M -> S (sandbox exists, need blocklist)
GAP-ECO-004 (Plugin Auto-Update): M -> S (versioning exists, need auto-update)
GAP-ECO-005 (Plugin Validation): S -> S (loader exists, need validate command)
GAP-ROUTE-002 (Effect Priority): M -> S (strategies exist, need priority queue)
GAP-PROMPT-006 (Instructions Hook): M -> S (adapter hook exists, need SDK generalization)
GAP-PROMPT-010 (Safety Framework): S -> S (critical rules exist, need reversibility)
GAP-MCPC-003 (Permission Relay): L -> S (relay exists, need wiring)
GAP-OBS-NEW-001 (Webhooks): M -> S (types exist, need HTTP delivery)
GAP-SEC-002 (Trust Classes): L -> S (sandbox exists, need TrustLevel field)
GAP-STATE-001 (Memory Extraction): L -> S (extraction exists, need prompt injection)
GAP-TOOLS-031 (MCP Resources): M -> S (client exists, need 2 agentic tools)
GAP-JSON-004 (Session API): M -> S (MCP tools exist, need unified REST)
GAP-OBS-003 (Prompt Observability): M -> S (strata metadata exists, need CLI command)
GAP-PROMPT-004 (Prompt Inspection): M -> S (strata data exists, need inspect command)

Blocked Gaps

Gap ID	Title	Blockers
GAP-STATE-002	Memory Consolidation	GAP-STATE-001 (memory extraction needs prompt injection first)
GAP-SESSION-005	Session Sharing	GAP-SESSION-002, GAP-REMOTE-003
GAP-PAR-010	Fork-Join Process Pattern	GAP-PAR-003, GAP-PROC-002
GAP-TOOLS-017	Git Worktree Isolation	GAP-PAR-001

Phase 3: Status Reclassification -- All Changes reference