What is the 'Neural Link'?

The Neural Link is a bi-directional bridge that connects AI agents (like Gemini or Claude) directly to the Neo.mjs runtime. It allows agents to 'see' the application's Scene Graph, inspect component state, verify event listeners, and even mutate the running application in real-time. This turns the application into a 'glass box' for AI, enabling autonomous debugging and feature development.

Why is Neo.mjs called an 'Application Engine' instead of a framework?

Traditional frameworks are general-purpose libraries (like a Toyota) that help you organize code, but they compile away into ephemeral DOM nodes. Neo.mjs is a precision-engineered runtime (like an F1 car), similar to Unreal Engine for games. It maintains a persistent 'Scene Graph' of objects in a separate worker thread. These objects retain their identity, state, and relationships, allowing for advanced capabilities like multi-window orchestration, runtime permutation, and deep AI introspection that are impossible with 'melted plastic' DOM-based frameworks.

What is 'Context Engineering'?

Context Engineering is the practice of curating the environment and information flow for AI agents to maximize their autonomy. In Neo.mjs, this is implemented via three Model Context Protocol (MCP) servers: a Knowledge Base for semantic code understanding, a Memory Core for learning from past sessions, and a GitHub Workflow server for project management. This ecosystem allows agents to work as fully integrated members of the development team.

What is 'Object Permanence' in the context of Neo.mjs?

In Neo.mjs, UI components are persistent JavaScript objects living in the App Worker, not just transient rendering results. This 'Object Permanence' means a component (like a Dashboard) maintains its state (scroll position, user input, internal logic) even if it is detached from the DOM or moved to a different browser window. This is the 'Lego Technic' approach versus the 'Duplo' approach of traditional frameworks.

What is an 'Agent Operating System'?

Neo.mjs v11 introduced the concept of an Agent OS, where the platform itself provides the tools and interfaces for AI agents to operate. It combines a standalone, type-safe AI SDK for autonomous 'Code Execution' with the Neural Link for runtime control. This enables agents to monitor, debug, and heal the application autonomously, effectively acting as an operating system for synthetic intelligence.

How does Neo.mjs handle multi-window applications?

Neo.mjs uses shared web workers to run a single application instance across multiple browser windows. All windows share the same application state and data in real-time. Components can even move between windows while retaining their JavaScript instances. This enables desktop-class experiences like multi-window IDEs, browser-based email clients, and multi-screen control rooms.

What makes Neo.mjs different from React, Angular, or Vue?

Neo.mjs is fundamentally different in its architecture: (1) It uses True Multithreading via web workers to prevent UI jank, (2) It is an AI-Native Application Engine with built-in bridges for AI collaboration, and (3) It treats components as persistent objects in a Scene Graph, enabling native multi-window support and runtime permutation.

Backlog

12114 Provider-agnostic context-limits via localModels.{chat,embedding} role-keyed split + retire SessionService hidden default
12091 SemanticGraphExtractor friction telemetry — detect empty-response distinct from parse-failure + skip retry amplification
12106 Stage 4: services + MCP-server codemod (A/B/D-prod/E sub-classes ~50-70 sites)
12105 Stage 3: orchestrator codemod — delete 16 delegation getters
12103 Stage 1: BaseConfig extends state.Provider + Option F 5-sub-point contract
12101 Greenfield aiConfig: meta-leaf tree + Provider extension
12109 Remove KB health table from Sandman handoff
12108 Stage 6: delete legacy ai/BaseConfig.mjs applyEnv() path
12107 Stage 5: retract Env.mjs consumer-facing exports + JSDoc anti-doctrine
12104 Stage 2: rewrite ai/config.template.mjs to meta-leaf tree
12102 Stage 0: extend initServerConfigs.mjs with overlay-preserving template advancement
12088 Sub 2 Phase 2 — REM run/stage state model JSONL writer + per-phase wall-clock + cadence-overflow detection
12097 Orchestrator config-as-SSOT enforcement: collapse env-or-config getters into envBindings, drop in-code env reads + resolver bypasses
12070 Sub 4: runSandman.mjs delegation refactor with CLI mode-selector
11871 Env-primitive deduplication + shared MCP stderr logger
12069 Sub 3: Unified executeRemCycle() orchestrator method
12087 Sub 2 Phase 1b — MCP exposure of 5-axis REM observability primitive + doc scaffold
12072 Sub 6: Provider-readiness substrate + rich diagnostic + decay placement
12090 Provider multi-model coexistence mandate — Ollama + OpenAiCompatible defaults ensure chat + embedding stay resident
12089 Provider keep_alive symmetry: Ollama + OpenAiCompatible default to -1 (ChromaDB-style service primitive); fix cadence-vs-keep_alive invariant
12094 Cross-repo env-var documentation follow-up for PR #12092 + PR #12093 (cloud-deployment guides + downstream-deployment env-example + README)
10284 MailboxService.addMessage silently succeeds when routing edges are culled — add post-linkNodes verification
12012 Orchestrator hard-exits on missing sqlite — initializeDatabase should self-bootstrap or fail-with-clear-log
12047 initServerConfigs: preserve operator edits when materializing stale server config imports
12078 Delete dead `ai/scripts/runners/runGoldenPath.mjs` — zero callers; superseded by direct Orchestrator → GoldenPathSynthesizer wiring
12067 Sub 1: Silent-failure root-cause investigation across 13 hypotheses
12074 Sub 8: Benchmarking gemma4 + context-window reuse research
12063 Raise OpenAiCompatible contextLimitTokens to match gemma-4 native 256K
11930 check-shorthand.mjs — substrate gate against verbose `key: key` regression (#11306 AC2 follow-up)
12013 AGENTS.md §edge_case_triggers wake-heartbeat trigger: 'halt state' binary + 'ZERO own-PRs' metric mis-shape the actual failure mode
12059 Fix Sandman graph provider routing
12068 Sub 2: 5-axis observability primitive + REM run/stage state model
11908 Sub 4: Layer 5 — sunset-handoff pickup queue (sandman-handoff-format.md extension)
11829 Multi-strategy wake-driver substrate: prevent agent idle-out via content + delivery + skill + metadata layers
12065 [Epic] Orchestrator-as-SSOT for the REM (Sandman) Pipeline
12080 Patch `Ollama.stream()` to inject top-level `keep_alive` (mirror `Ollama.generate()` line 108)
12071 Sub 5: Standalone refreshGoldenPath() orchestrator method + npm script
9959 fix: Memory Core semantic search crash & active session summarization leak
12075 Sub 9: Regression test coverage for 13 silent-failure modes
12073 Sub 7: Hierarchical-summarization strategy (chunking-aware Tri-Vector)
12066 Unify REM pipeline under Orchestrator SSOT
10349 Sunset Protocol: self-DM handover for next-session boot pickup
11791 Operator docs + health/telemetry for tenant-repo ingestion
12052 Day0Tutorial Milestone 6: rewrite to first-class pull mode
12051 bootstrapWorktree: hydrate Tier-1 + materialize per-server configs (Discussion #12049)
12036 Cloud tenant-repo CLI sync: 3 Day-0 substrate gaps
12039 KB_REVISION_BOUNDARY_INVALID on first tenant sync (null baseRevision)
12040 Tenant-repo ingestion: add branchRef to tenantRepos[] schema
12042 Real-resolver smoke for TenantRepoSyncService export-drift escape
12048 bootstrapWorktree duplicates initServerConfigs without materialize-on-copy
12032 GitMirror credentialRef: support file: scheme for tenant secrets
12033 Extract ingest_source_files facade from KB tool mapping
12038 Document @me assignee alias on create_issue
12028 Orchestrator backup task label misleadingly cites 'memory core' only
12029 Add default raw-ingest Source for tenants with unknown repo shape
12015 Day-0 prerequisites lack macOS container-runtime alternatives
12026 Dockerfile.dockerignore drops KB content paths needed for in-container Neo-shared ingestion
12025 Orchestrator healthcheck probes wrong filename (state.json vs orchestrator-state.json)
12023 Dockerfile.dockerignore drops integration test fixtures
12022 Day-0 Caddyfile bare :443 prevents tls internal cert issuance
12019 Cloud-mode orchestrator: spawn chroma ENOENT loop on first boot
12017 Missing root .dockerignore: ai/deploy build context inflates to 90 GB
12016 Compose: quote interpolated cpus/memory in local-model service
12014 Orchestrator daemon refactor left stale path references
11948 Sub of #11837: workspace-safety integration test (Sub-5 AC5 follow-up)
12007 DreamService.spec.mjs — 2 tests failing on dev (synthesizeGoldenPath + malformed-JSON-retry)
10172 Graph node-ID case canonicalization: settle memory:/MEMORY: and session:/SESSION: convention
10158 Memory/Session graph nodes: post-ship telemetry + retention policy
10150 Mailbox: optional Chroma semantic layer for "find related messages"
11965 Wire provider routing and native Ollama runtime paths
10034 Concept Graph Visualization App
11603 Substrate bandwidth: 97.5% META / 0% Body-pillar over last 200 merged PRs — counter-bias mechanism needed
11604 Substrate governance: skill bloat from premature codification — codify-deferral discipline
11605 Compress skill baggage into decision-atom maps
11735 Tenant-source inventory + parser coverage deepening (post-MVP cloud deployment)
11795 Explore Codex external-model routing for 1M context
11812 Claude sibling identity and instance wake routing
11816 Measure Claude sibling provider-capacity independence
11821 Define Claude sibling identity contract
11822 Implement Claude sibling instance wake routing
11906 Sub 2: Layer 1 — wake-content enrichment (content-rich heartbeat prompt, milestone-agnostic)
11909 Sub 5: Layer 4 — structured wake metadata schema extension (DEFERRED)
10293 P6a: Neo Tenets v0 document — AGENTS_TENETS.md authoring
9915 [Blocked Research] Moltbook API / identity feasibility for Neo AgentOS demo
9295 [Blocked Epic] Autonomous Neo Agent Demo after Moltbook API and identity research
9296 [Blocked] Autonomous agent action sandbox after cloud and Moltbook shape
9298 [Blocked] Moltbook demo agent after API and identity research
9297 Implement Programmatic Email Identity for Agents
11993 Wake substrate evolution: 3-signal model + Shape B heartbeat pulse
9299 Implement Agent Self-Discovery via Neural Link Introspection
10136 Rewrite CodebaseOverview.md to reflect Two Hemispheres architecture + Dream Pipeline
10139 Extend Memory Core with Explicit A2A Primitive
12008 Consolidate wake evaluator paths: bridge-daemon delegates to WakeSubscriptionService (single source of truth)
12003 Add active-a2a-participants target source for activity-derived pulse candidate discovery (Epic #11993 follow-up)
10292 P1: Content Provenance Tracking — authoredBy edges + 8-tier trust taxonomy on Memory Core
12005 Delete daemon.mjs router dead code; consolidate mlx/lms config into Orchestrator getters (thin-Orchestrator completion)
10476 P8: External Link Quarantine & Stealth-Intent Detection (Anti-Astroturfing)
11994 Sub-i: WakeSubscriptionService.emitHeartbeatPulse + ADR 0002 §6.1.6 update
11981 [Sub-2 of #11976] Add KB test-fixture (KB_DEFAULTS) + migrate SourcePathsConfig drift-vulnerable assertion
11990 SwarmHeartbeatService delivers pulses via tmux injection — Codex Desktop never wakes
11996 Sub-iii: Remove tmux-inject + Shape A heartbeat-mailbox path; wire SwarmHeartbeatService to emitHeartbeatPulse
10103 Agent OS config ownership: Tier-1 deployment defaults
11995 Sub-ii: 3-signal wake derivation + orchestrator-local backoff + readiness-sentinel parser
10126 Remove stale aiConfig.engines.neo consumers from maintenance scripts
11986 Restore lms server lifecycle supervision in orchestrator (regression #11093)
10270 ChromaManager: log operator-actionable error before boot-time Chroma config throw
10125 Reconcile aiConfig.architecture reads vs engine config key
11983 Remove config-template test fallbacks and legacy env hooks
11872 Fix Codex nightshift wake driver gap in Orchestrator heartbeat
11977 [Sub-1 of #11976] Add Tier-1 test-fixture (TIER1_DEFAULTS) + migrate top-level ai/config.mjs imports in tests
11973 Bump SourceParser acorn ecmaVersion to support ES2025 import attributes
11976 Tests import config.mjs (operator-overlay) instead of config.template.mjs (canonical defaults) — drift risk across ~78 imports
11964 Prove cloud provider readiness for embeddings, chat, and dream
11968 Fix config.template.mjs imports across runtime code + clean JSDoc ticket-archaeology from #11966 / #11967
11942 Sub-of-#11790: tenant-repo-sync residuals (jitter/backoff + concurrency-gate + KB_TENANT_REPO_SYNC_ error codes)
11963 Map Agent OS config defaults into Tier-1 AiConfig
11955 Retire task-name-constant indirection in ai/daemons/orchestrator/TaskDefinitions.mjs
11075 Exploration: Migrate orchestrator magic numbers + retention constants to ai/config.template.mjs
11954 Rename acme/* placeholders to neomjs-owned across cloud-deployment docs + test fixtures
10291 Organism self-defense substrate for cloud-phase #9999 deployment
11834 Sub 2: Orchestrator test-fixture + invariant coverage for new config substrate
11790 tenant-repo-sync scheduler lane — periodic + manual
11864 Sub 20: Harmonize existing Coordinator services to scheduling/.mjs pure-function pattern
11923 Clean KB and graph source-comment archaeology
11133 GH-content sync: workflow-fragility — local branch-discipline gap producing stale-branch + chore-sync contamination (5x same-session pattern)
10311 Institutionalizing Swarm Autonomy (Phase 1: REM Sleep & A2A)
10517 Define HarnessPresence and wakePolicy routing for A2A wakes
10627 Steady-state set_session_id rotation in resumeHarness boot-grounding flow
10788 Validate + lock Claude recovery target as Claude Desktop Tab 3 (resolve resumeHarness.mjs:287-291 TODO)
11179 Implement Boot-Time Pre-Flight and Hard-Refusal Predicate for Sandman Handoff
11372 Epic: Universal Ordinal-100 Content Architecture (ADR 0004)
11602 Substrate discipline: monkey-patch vs root-cause analysis — anti-pattern naming + V-B-A gate
11950 Inventory skill baggage for decision-atom rollout
11924 Clean GitHub Workflow and shared MCP source comments
11925 Clean daemon script and config source comments
11937 docker-compose.yml: add orchestrator + ingress healthchecks for cloud-deployment trial operator visibility
11789 Diff-to-ingest envelope builder for tenant-repo sync
10143 Graph-first Memory artifacts: lift Memory + Session to first-class nodes
11116 Epic-shape discipline: separate code-change commits from data-migration commits in PRs
11102 epic-resolution Verdict-Authority calibration: peer-V-B-A consensus suffices for epic close
11111 ChromaManager dedup: extract shared Chroma-client primitive (M6 retrospective)
11830 Layer 2: implement resolveSwarmHeartbeatTargets() deployment-portable resolver for SwarmHeartbeatService
11306 Collapse verbose `key: key` shorthand in object literals (~71 instances)
11144 ai:restore Chroma preserve-live parity for #importMemories (follow-up to #11141)
11798 ideation-sandbox-workflow.md §6: family-keyed quorum + AUTHOR_SIGNAL
11912 Clean ai source-comment archaeology
11922 Clean Memory Core source-comment archaeology
11900 Sub 18 Phase 2: CadenceEngine.runIfDue drop + dispatch switch + Sub-13 cleanup + test collapse
11905 Sub 1: Layer 2 — heartbeat target resolver (BLOCKING; resolveSwarmHeartbeatTargets contract)
11902 Inventory skill-runtime baggage for decision-atom migration
11907 Sub 3: Layer 3 — per-turn anti-pattern surface (AGENTS.md + peer-role-mode.md)
11904 Pilot cycle-aware pr-review density compression
11884 Codify decision-atom lesson promotion
11890 Codify why-first source-code documentation contract
11895 Require next-lane pickup while CI is pending
11893 Compress PR-review hot path with deletion-first templates
11878 Shared MCP stderr logger primitive
11788 GitMirror primitive + persistent mirror acquisition service
11874 Restore core.Base contract in SwarmHeartbeatService — drop external initAsync calls + isInitialized band-aid
11787 Tenant-repo config + credentialed repo-access contract
11882 Require surface-anchor V-B-A for Contract Ledger rows
11873 Env-primitive deduplication: EnvConfig.mjs deletion + MCP migrations + Orchestrator scoped-binding
11885 Make PR review circuit breaker enforce micro-delta reviews
11886 Tighten PR-review Micro-Delta Circuit Breaker + add author-side parity
11817 Standardize AI script CLI parsing on Commander
11731 Server-side tenant-repo ingestion for cloud Agent OS deployments
11870 Unified config + env substrate consolidation
11855 Sub 14: Centralize env-binding registry — ai/config/env.mjs + dotenv lift
11861 Sub 19: Extract MaintenanceBackpressureService — heavy/golden predicates + deferral recording + lease/dependency executor wrappers (B-prime)
11860 Sub 17: Extract GoldenPathCoordinatorService — due/dependency trigger only, synthesizer stays as execution service
11859 Sub 16: Extract SwarmHeartbeatCoordinatorService — getDueTask only, initAsync stays in service
11858 Sub 15: Extract DreamCoordinatorService — getDueTask only, due-trigger selection only
11854 Sub 13: Collapse over-engineered Orchestrator Service-DI (Class C field deletion + historical-context comment strip)
11862 Sub 18: Orchestrator generic registry wire-up + CadenceEngine pure-trigger-builder correction + collector/pickNextCandidate (Round-2 closer)
11848 Sub 12: Collapse buildScripts/ai/ into ai/scripts/{maintenance,migrations,diagnostics,runners,setup}/
11847 Sub 11: ai/scripts/ thematic split (lifecycle/maintenance/migrations/diagnostics/runners/setup/lint)
11846 Sub 10: Cross-daemon services bucket (ai/services/graph/ + ai/services/ingestion/)
11845 Sub 9: Sub-daemon cluster co-location (bridge + kb-alerting + kb-gc + kb-reconciliation) with daemon.mjs naming
11844 Sub 8: Orchestrator-cluster co-location (ai/daemons/orchestrator/) + daemon.mjs naming + test mirror + package.json
11827 Tech-debt: hardcoded DEFAULT_X constants bypassing ai/config.template.mjs substrate (5+ surfaces)
11835 Sub 3: Removal of DEFAULT_* constants + parser surfaces made obsolete by Orchestrator refactor
11833 Sub 1: Orchestrator masterclass-reference refactor (4-way Service-DI + 2-value chain + configure() removal)
11840 Sub 7: Bump swarmHeartbeatMs wake interval 5m → 15m
11832 Sub 6: Neo.util.Env THIN substrate primitive (lift EnvConfig.mjs parsers to src/util/Env.mjs)
11837 Sub 5: External-user configurability audit (forks, npx neo-app workspaces, non-Neo-team clients)
11836 Sub 4: Sibling daemon propagation of masterclass-reference pattern (5-6 daemon files)
11831 Orchestrator.mjs masterclass-reference: 4-way Service-DI classification + Neo.util.Env substrate + 2-value chain
11819 Allow null `from` in mailbox latestPreview schema for system messages
11824 Make idle-out nudges lifecycle-actionable
11308 Enforce v13 project attachment unconditionally in /ticket-create workflow
11803 Tier-2 revalidation-trigger mechanism (OQ5 from #11793)
11260 Substrate-relocation: move Sandman Handoff Pre-Flight body from AGENTS.md §22 to new `/sandman-handoff-pre-flight` skill
11649 Per-substrate retention policy configuration for KB/MC backup mechanisms
11807 Add Codex hooks feature-flag migration guard
11730 Cloud Agent OS Deployment — Post-MVP Residual Workstreams
11811 Normalize KbAlertingService alert sender identity
11797 Validate orchestrator swarm-heartbeat wake delivery
11796 Active-peer quorum for high-blast graduation consensus
11801 Mirror family-keyed quorum into AGENTS.md §swarm_topology_anchor
11800 Mirror family-keyed quorum into pull-request-workflow.md §6.1.1
11799 ideation-sandbox-workflow.md §6: family-keyed quorum + AUTHOR_SIGNAL
11802 identityRoots.mjs: add participationStatus structured field + seed migration
11740 Amend ADR 0014 for pull-based KB ingestion
11785 Codify ADR successor-risk and challenge classification
11783 Skip no-op KB cascades after primary dev sync
11780 Update Codex hooks feature flag
11732 Graph-store evolution — SQLite to networked SQL (post-MVP, D5)
10015 [Sub-Epic] Dynamic Topology — Unified vs. Federated Routing
10186 MCP concurrency audit + single-writer enforcement
10016 [Sub-Epic] Multi-Tenant Identity & Data Privacy
10669 Wire @neo-gpt / Codex Desktop into resumeHarness identityMap + HARNESS_REGISTRY
10945 Expand deployment-pipeline integration coverage for Memory Core
10950 Reconcile topology matrix coverage for Memory Core deployment
11775 Extract reusable Windows batch spawn helper
11733 Downstream external deployment-pipeline wiring (post-MVP cloud deployment)
10684 Support cross-platform execution for antigravity-cli prompt injection
11767 Handle Antigravity .cmd execution on Windows
11734 Optional local-model runtime container profile (post-MVP, D0-gated)
11768 GitLab-workflow MCP server scaffold
11766 Fold the swarm-heartbeat into the Orchestrator as a local-only lane
11736 Broader deployment guide + security hardening beyond the MVP (post-MVP)
10776 Surface follow-ups from peer review in PR body Follow-ups block (do not lose at merge)
11720 Cloud Agent OS Deployment Readiness
11725 Deployed healthcheck + production-shaped journey proof
10633 Derive AllAgentIdleSignal cycle_id from all-idle state, not pulse timestamp
10757 Cognitive-load audit cycle 2 — mutation gate + periodic cron + MCP tool surface
10795 Convert wake-substrate CLI-shape scripts to dual-mode (CLI + module-export) so SwarmHeartbeatService imports replace subprocess hops
10763 Codify Night-Shift Swarm Momentum and Leased Driver Pattern
11728 Day-0 executable cloud-deployment tutorial
11364 Retire PR archiveVersion metadata carry-forward
11752 Reference the manage_discussion tool in ideation-sandbox §3
11743 Specify repo-push receiver and auth flow for KB ingestion envelopes
10138 Add manage_discussion MCP tool for GitHub Workflow server (body update support)
11724 Production reference deployment profile + compose
11744 Gate ingest_source_files exposure by transport
10702 Extend get_conversation to issues (selector parity with PRs)
11727 DeploymentCookbook realignment as accurate deployment authority
11719 Fix broken Section 6 table in Deployment Cookbook
11723 Production container topology — multi-container + resource limits
11722 Top-level ai deployment + maintenance-policy config
11726 Tenant-repo ingestion operational model for cloud deployment
11721 Cloud deployment topology + scheduler-task-taxonomy ADR
11729 Cloud deployment ADR set — D1/D3/D4 decision records + stale-ADR reconciliation
11624 Cloud-Native KB Ingestion for External Workspaces
11628 KB Ingestion Phase 4: Operations + Observability for Cloud-Native Deployments
11643 KB Ingestion Phase 5: Integration + Unit Test Parity with Memory Core
11716 Audit kb-config daemon readability under GraphService RLS
11641 Phase 4C — Stale-Chunk Garbage Collection Daemon: Orphan Detection + Retention Enforcement
11711 KB reconciliation: force-push & manifest-orphan drift detection
11626 KB Ingestion Phase 2: Ingestion Service + MCP Small-Batch Facade + Bulk Facade
11712 Add a server-stamped ingestedAt timestamp to tenant KB chunk metadata
11640 Phase 4B — Manifest Reconciliation Daemon: Tenant-State vs Chroma-Actual Sync
11627 KB Ingestion Phase 3: Cloud Deployment Guide + Worked Examples
11642 Phase 4D — Operator Alerting Surface: Telemetry Thresholds → A2A + External Notification
11639 Phase 4A — Per-Tenant Ingestion Observability Daemon (KBRecorderService Extension)
11645 Phase 5B — KB Tenant Isolation Integration Tests (post-Phase-0/1D)
11638 Phase 2F — Test Fixture Infrastructure: Synthetic External Workspaces + Multi-Tenant E2E Suite
11701 collection.Base: isItem() treats null as an item
11637 Phase 2E — Q5 Tenant Config Storage: Native Edge Graph Extension
9208 Investigate Playwright OffscreenCanvas Performance on Desktop
9209 Benchmark Grid Scroll-to-Update Latency
11705 Collection.isItem should not classify null as an item
11698 Sandman hides apoptosis null-node failure as success
11635 Phase 2C — Bulk Facade: CLI ai:ingest-tenant + Streaming Ingestion Path
10077 [bug] manage_issue_labels MCP tool fails on PRs — uses Issue-only GraphQL lookup
11693 Golden Path ranks closed Discussions as open
11636 Phase 2D — Q12 Search-Hydration Mode Resolution + SearchService Implementation
11691 Remove human override from sandbox liveness graduation
11687 Add cross-server MCP boot and listTools smoke coverage
11182 Wake subscription duplicate-accumulation + GPT zero-delivery (post-#10624 recurrence)
11110 github-workflow MCP needs systematic boot + wiring + integration test coverage
11307 Add merge-conflict-safe lane audit to post-review-pickup discipline
11634 Phase 2B — MCP Facade: ingestSourceFiles Tool + #10572 Work-Volume Gate Threading
11685 Harden KB shadow-swap before activation
11683 KB re-embed: shadow-collection swap, not in-place gut-and-rebuild
11680 getNeighbors omits semanticVectorId; pre_brief_session hydration inert
11679 Phase 2C — Bulk KB Ingestion Facade with bulk-mode Gate Bypass
11633 Phase 2A — KnowledgeBaseIngestionService Core: Orchestrator + parsed-chunk-v1 Validation + Delta Integration
11625 KB Ingestion Phase 0/1: Contracts, Source/Parser Registry, KB Tenant Isolation
11630 Phase 0/1B — Source/Parser Registry Extraction + Per-Source Path Externalization + Byte-Equivalence Fixture
11671 Add AGENTS.md rule 7 pointer for broadcast fallback
11632 Phase 0/1D — KB Tenant Isolation Read-Side: QueryService/SearchService where-Filter + Fail-Closed Test Suite
10900 Support SSE and HTTP transports in Neo.ai.mcp.client.Client
11669 Clarify broadcast-suppressed lane pickup fallback
10011 Native Edge Graph (SQLite): Row-Level Security & Tenant Isolation
11660 KB Ingestion Phase 0/1B-β: Externalize per-source paths to aiConfig.sourcePaths
9872 Grid Multi-Body: 3-Tier Component Orchestration and Architecture Refactoring
11631 Phase 0/1C — KB Tenant Isolation Write-Side: VectorService Server-Stamping + Tenant-Aware chunkId + Spoof-Rejection
11646 Phase 5C — KB Unit Test Coverage Expansion (close 32-vs-12 parity gap with MC)
11663 KB Ingestion Phase 4: Configurable bundle retention policy via aiConfig.backupRetention
11665 KB Ingestion Phase 4A: Multi-tenant ingestion observability daemon scaffold + telemetry schema
11658 KB Ingestion Phase 0/1B: Source/Parser registry + useDefaultSources/useDefaultParsers configs
11653 KB importDatabase rejects backups with `document: null` (steady-state KB shape)
11652 Substrate-layer guard: refuse canonical Chroma collection delete without UNIT_TEST_MODE
11654 bootstrapWorktree: prune stale `.claude/worktrees//` after branch merge
11650 FileSystemIngestor missing .claude + .codex from ignorePatterns; 3.1M stale FILE/DIRECTORY/CONTAINS graph elements
11644 Phase 5A — KB MCP Server Integration Test Parity with MC (pre-Phase-0/1 shippable)
11629 Phase 0/1A — Ingestion Contracts: parsed-chunk-v1 + backup-record-v1 + Path-Identity Tuple + Tombstone Spec
11447 Brain-Pillar Consumer-Friction Feedback Channel (Visibility-Only V1)
10755 Codify Resolves/Fixes (preferred) vs Closes (avoid for shipped work) in pull-request-workflow + DreamPipeline doc
11619 Document Neo test bootstrap import pair in unit-test skill
11617 Fix standalone ai/scripts specs failing setup Neo.ns mock
11402 [Memory Core] Support lightweight lms server start in TextEmbeddingService
11417 Reject or resolve invalid to: in add_message instead of silent null-storage
11608 Phase 2 of #11599: AGENTS_ATLAS.md heading conversion + AGENTS.md cross-ref simplification
11596 Golden Path misses embedding dimension drift
10117 DevIndex: 354 users.jsonl entries absent from tracker.json
11455 Expand post-review-pickup trigger surface (Discussion #11423 Phase B Option B.1-prime)
11601 Substrate decision: Model-Stats ADR — capability/limit/sunset/promotion framework
11584 Restore Map/Atlas compaction: revert #11571 + ADR 0011 + lint cleanup
11594 IssueSyncer re-classifies unchanged closed issues — persistent ARCHIVE ANOMALY WARN on #7910
11595 Graph apoptosis rollback re-adds node IDs as strings
11609 Add role-first lane pickup before review intake
11599 Substrate-wide `## §semantic_concept_name` heading form for all agent content
10494 Fix DreamService token exhaustion and enforce PR priority hierarchy
11590 Allow generated-only dev sync commits in chore hook
11593 Codification spot for cross-family substrate-pattern memories (harness-private vs shared)
11591 Restore 'semantic anchor' term in ADR 0011 (concept-based meaning)
11585 Retry transient GitHub GraphQL failures during sync
11558 Substrate Numbering Semantic Anchor Migration
11562 Migrate workflow skills to semantic anchors
11564 Migrate ADR and docs refs to semantic anchors
11582 Restore direct-dev GitHub workflow sync auto-push
11404 Epic: GitLab Workflow MCP Server (parity with gh-workflow for issues + merge requests)
11578 Extend unit-test setup.mjs to mock Neo.Main and addon.LocalStorage
11580 Fix sync-data hook for automated commits and repo-local branch checks
10206 feat(memory-core): add harness classification to boot-time sibling-PID logging
11561 Migrate AGENTS maps to semantic anchors
11573 DiscussionSyncer: synced markdown lacks `closed`/`closedAt` despite #11554 — V-B-A post-merge verification gap
11560 Add semantic-anchor lint for agent refs
9185 Implement Telemetry Probe for Worker Saturation Monitoring
11115 Institutionalize Safeguards Against Chore-Sync Contamination in Feature Branches
11563 Harness-Scratch `.gitignore` Extensions
11501 Apply visible+invisible anchor pattern + skill-pointing errors to PR-body lint surfaces (cross-surface enhancement)
11442 Intercept mechanical hygiene defects via pre-commit hook (Husky/Lint-Staged)
11559 Author semantic-anchor policy ADR
10050 Concept Description Enrichment: Source-Grounded Semantic Anchors
11556 AGENTS.md non-contiguous section numbering — audit + decide treatment
11554 Sync `closed` + `closedAt` to Discussion frontmatter in DiscussionSyncer
11552 Resolve stale AGENTS.md §-references in skill substrate post-#11551
10295 P2: Trusted-Instruction Ring — AGENTS.md §14 insertion + cross-skill references
11548 Operationalize Sandman handoff symlinks for active clones
11537 Implement precondition and post-verify semantics for [lane-intent] and assignee mutations
11500 Cleanup Memory Core 8001 substrate residuals post-ADR 0003
11546 Codify Collapsed-N/A audit conciseness rule in pr-review templates
11549 Remove AGENTS.md Section 21 (Workflow Skills) via Frontmatter Parity
10148 Mailbox: archiveMessage / deleteMessage + retracted-marker semantics
11516 Repair DevIndex users/tracker reconciliation and rename recovery
11538 Playwright component tests timeout on empty viewport visibility
9498 Grid Multi-Body: Infinite Canvas Cross-Window Column Drag & Drop
9499 Grid Multi-Body: Test Suite Refactoring & Expansion
9865 Multi-Body: Centralize Selection Model Orchestration in GridContainer
9939 Epic: Autonomous Worker Dispatcher Pipeline (RLAIF Phase 2)
10635 Institutionalize MX-Loop Lost-Concept Recovery
11256 [Epic] Proactive architecture-decision substrate: /turn-memory-pre-flight + /architecture-pre-flight
11411 Resolve Antigravity 24KB Memory Limit via Progressive Disclosure
10008 Playwright Test Coverage: Unified Monolithic Topology
10537 Modularize pr-review-guide.md condition-gated audits
11319 [Epic] Trigger-Aware Workflows: Per-Section Triggers Apply Map vs World Atlas Recursively (Discussion #11314 graduation)
11317 Skill Semantic Search Ingestion Pipeline
10960 v13 Release Tracking — main-focus-items canonical sub-issue tree
11503 Enforce heavy-maintenance mutex across Agent OS tasks
10982 Migrate per-server MCP services to flatter SDK structure
11531 Codify PR Diff === PR Body mental model as a 1-liner in AGENTS.md
11533 Codify "PR Diff === PR Body" mental model in AGENTS.md
11542 Normalize AGENTS.md GitHub links to short-form #NNNNN (byte-budget compaction)
11529 Harden testing skill triggers for custom Playwright configuration
10180 Mailbox polish: countMessages primitive + concept provenance docs
11519 Cross-daemon lease coverage: orchestrator-side shared-lease adoption + env-var child inheritance
11524 Separate MLX launch model from OpenAI API label
10010 Memory Core: Team vs Private Context Retrieval Flag
11520 Lane D of #11503 — annotate PrimaryRepoSyncService.runKbSync cascade as observable kbSync task
11513 Lane A of #11503 — add `backup` to DEFAULT_HEAVY_MAINTENANCE_TASK_NAMES + cross-poll deferral tests
11515 Add release-timing consumer-guidance to HeavyMaintenanceLeaseService JSDoc + reference-impl example
11507 Lane C of #11503 — wrap manual heavy maintenance scripts with HeavyMaintenanceLeaseService
11511 Classify Golden Path as light orchestrator maintenance
11508 Modernize CI workflows: Upgrade github-script to v9 and remove obsolete Node 24 overrides
11495 CI lint for gh-CLI-direct PR review bypass (split from #11492 per GPT V-B-A narrowing)
11505 Add shared heavy-maintenance lease primitive
11504 add_message MCP tool silently accepts invalid recipient strings — substrate-evolution to mechanical reject
11491 Promote manage_pr_review MANDATORY pre-step from description-prose to JSON-schema body-shape validation
11406 Add CI grep-fail check for retired-primitive imports
11492 Tool-boundary body-shape validation for PR creation (pull-request skill bypass companion to #11491)
11496 Orchestrator still starts Memory Core Chroma after ADR 0003
11487 Add orchestrator maintenance backpressure
11486 IssueSyncer ARCHIVE ANOMALY emits thousands of false-positive WARN during ADR 0004 clean-cut
11493 CI PR-review-body lint for pr-review skill adherence (CLI bypass defense)
5854 Learn Content: Custom Events => adding listeners procedurally
5822 main.addon.MonacoEditor: remove editor/editor.main.nls.js
5756 src/MicroLoader.mjs: replace the fetch() call with a json module import, once firefox added support
5728 worker.App: onOrientationChange() => limit the scope to affected windows
5705 Getting Started => Setup needs a rewrite
5698 tooltip.Base: singleton mode => honor nested themes
5619 core.Base: setStaticConfig() => evaluate if we can remove the staticConfig part
5598 selection.Model: select() => add support for widgets using a collection instead of a store
5577 worker.mixin.RemoteMethodAccess: accessing new main threads too early
5134 Creating a first Storybook story to render a neo.mjs button
5133 Creating the neo.mjs renderer for Storybook
5132 Creating the Storybook framework
5010 Storybook integration for neo.mjs
11484 Downgrade per-item Created/Moved/Updated sync logs to DEBUG (#11477 follow-up)
10605 Compact redundant priority in wake digests
11481 IssueSyncer #formatIssueMarkdown null-safety + comprehensive unit-test sweep (#11474 follow-up)
11477 Reduce per-issue log volume during gh-workflow sync (downgrade per-item INFO to DEBUG + add batch-summary checkpoints)
11478 Enforce pr-review skill read in manage_pr_review tool description
11474 IssueSyncer #formatTimelineEvent crashes on null assignee/label/subIssue/parent/etc (defensive null-safety needed)
11328 Audit epic-review + epic-resolution skills for Discussion-graduation enforcement gaps
9999 [Epic] Cloud-Native Knowledge & Multi-Tenant Memory Core
11469 Add `ai:sync-github-workflow` npm script wrapping `GH_SyncService.runFullSync()` for CLI invocation
11471 Orchestrator MLX task starts stale Gemma 2 model
11413 Execute Progressive Disclosure Migration for AGENTS.md
11463 Fix YAML parser errors in SKILL.md frontmatter
11467 Delay PR review requests until CI is green
11459 Classify orchestrator child stderr and throttle skip noise
11465 Add CI fail-fast gate before formal PR review
11464 fix(ai): wrap YAML frontmatter descriptions in quotes to prevent parser errors
11451 Clean-slate migration: Delete existing substrate + run sync_all (ADR 0004 Phase 1 Task 10)
11457 Fix Substrate Size Guard failure (AGENTS.md > 24576 bytes)
11448 Codify Antigravity scratch-path allowlist
11334 Refine SkillSource sub-rule metadata via trigger pointers
11441 Add review-loop cost circuit breaker
11412 Implement Substrate Size Mechanical CI Guard
11453 Capture gold/blocker vocabulary in ADR 0007
11187 Adopt single-root archive with lazy 100-item chunking (Discussion #11180 graduation)
11435 ADR 0007 amendment: §21 trigger entries as Recursive-Reload Anchor (post-pruning-discipline-recall)
11437 Block skill-lint growth into oversized workflow maps
11433 FAIR-band stance declaration as PR-open Pre-Flight Gate (#11432 follow-up; bypass-resistance)
11427 Implement ADR 0008: SKILL.md Anatomy and Authoring Contract
11405 Release-notes chunking: new ReleaseNotesSyncer
8920 Feat: Implement Neo.component.markdown.VDom (VDOM-Native Parsing)
8921 Feat: Implement Neo.ai.Chat (Reference UI)
8922 Feat: Implement Neo.container.Spatial (Pan/Zoom Whiteboard)
8925 Epic: Implement Specialized Agent Workflows (.agent/workflows/)
9159 regression: Component Columns trigger insertNode operations during scrolling
9160 test: Implement Computational Budget assertion in Grid Pooling tests
11445 Expose updateDiscussion body mutation in gh-workflow MCP
11422 Phase B: Hardening SKILL.md Description-Routers
11430 Codify FAIR-band author-lane pickup discipline
11420 Phase A: Extract Compaction Taxonomy to ADR 0007
11425 Separate ADR 0005 approval semantics from human merge gate
9891 feat: Strategic Constraint Nodes for Golden Path directional control
9890 feat: DreamService 4th REM Vector — executeNLActionDigest()
10462 Graph-integrity audit: verify SESSION→memory completeness post-REM
10420 fix(github-workflow): restrict notification preview to reason=mention in healthcheck
10219 Sandman active detector: stale assignments + recent open PRs
10164 Add pre-commit cross-PR file-collision check to author workflow
10120 Golden Path: external-visibility-gap signal + adaptive weighting
10096 [bug] GraphqlService.query discards partial data when GraphQL returns errors — breaks aliased batch queries
10094 [enhancement] Formalize InvalidationDetector interface for updatedAt-blind sync drift detection
11414 Antigravity Payload Capture and Cross-Harness Validation
11408 Delete obsolete migrate-substrate-11360 script
11390 Adopt contentPath index map in GH workflow syncers
11373 Add ADR + concept content types to Knowledge Base substrate
11361 Consumer-side ingestion: KB sources + MC ingestors recursive archive support
11400 Amend ADR 0004 with explicit Regeneratable-Cache Strategic Principle (§1.3)
11320 Skill manifest lint: per-file payload cap + section-trigger declarations (Sub-A of #11319)
11397 Amend ADR 0004 with explicit Clean-Cut Pattern + Deprecation-theater anti-pattern (§2.6 + §5.6)
11395 Broaden TextEmbeddingService model-unload retry to cover LM Studio 'Failed to load model' / 'Operation canceled' shape
11389 session-sunset Step 2: skip manual sandman invocation under convergent scope
11379 Consolidate chunkPath.mjs + archivePath.mjs into universal contentPath.mjs (ADR 0004 Lane A)
11393 Memory Core add_memory must retry-on-model-unload when embedding provider drops idle models
11363 Remove gh-workflow legacy archive config fallbacks
11380 Orchestrator daemon child process failures (stdio, mlx arg, chroma gap)
11385 Stale-reference cleanup in workflow-skill docs (issue-archive) (Epic #11372 Task 9)
11384 ProcessSupervisorService discards child stderr — capture per-task to enable failure triage
11383 Orchestrator should manage Memory Core Chroma daemon (port 8001)
11377 Implement ADR 0006: ADRs as Graph-Queryable Entities (specific ADR label)
11365 Restore milestone-aware routing capability in gh-workflow syncers
11367 Land ADR 0004: GitHub Content Architecture (universal ordinal-100 chunking)
11370 Codify optional ADR emission at Ideation Sandbox graduation (4-file substrate amendment)
11360 Substrate cleanup: legacy folders + 195-PR collision + active-tier residue + syncer fixes
10758 Add age-aware successor-risk audit to ticket-intake
11358 Epic #11187 Phase 0B: Fail-Closed Write Guard for SyncService
11309 [epic-followup] Orchestrator integration for dream daemon run history tracking
11351 [Agent Substrate] Enforce Upfront Discussion Criteria Mapping in ideation-sandbox and ticket-create (#11328 follow-up: optional ergonomics)
11349 [Agent Substrate] Enforce Source Discussion Criteria Mapping Gate in `epic-review` (#11328 Part 1)
11350 [Agent Substrate] Enforce Source Discussion Closeout Gate in `epic-resolution` (#11328 Part 2)
11347 Layer 3 of 4-layer PR-base defense: pr-review Cycle-0 baseRef verification gate
11342 Demote INV1 cascade detail to AGENTS_ATLAS
11345 Modify AGENTS.md §0 Invariant 7: atomic self-assign + broadcast `[lane-claim]` to AGENT:*
11322 Integrate SkillSource into ai:sync-kb Pipeline
11337 Forbid agent-authored PRs targeting main
11336 Add mechanical PR base branch guard to GitHub workflow
11323 Unit Tests for SkillSource.mjs
11332 Skill manifest lint: perFilePayloadBudget primitive (narrowing of #11320 AC1-3 + AC6-9; AC4-5 stay parented to #11320)
11321 Implement SkillSource.mjs for KB Ingestion
11310 AGENTS.md §0 Invariant 7: no code work without a self-assigned ticket
11326 Expose skill content type in KB MCP query schema
10837 Sharpen substrate mutation triggers to enforce Progressive Disclosure
11318 Identity Continuity and Embodied Episode Architecture
11313 Per-file size caps + atlas-monolith detection in skill-manifest-lint (extends #11275 enforcement scope)
10779 Healthcheck observability: features.dream block (autoDream + autoGoldenPath actual state)
11274 Neo.ai.Client missing handlers for get_namespace_tree, get_neo_config, and check_namespace
10209 test(github-workflow): implement contract-scan test for config completeness
11291 Migrate PR archives to versioned archive/pulls paths
11288 Validate archive migration and document anomaly hooks
11290 Fail loudly on stale GitHub Workflow archive config
11262 Implement XML-tag substrate for anti-drift anchors in AGENTS.md
11287 Cleanup consumer paths for TicketSource, SEO, and analyzers
11284 Collapse active discussions to flat structure
11286 Update CI pipelines and build scripts for new archive substrate
11285 Implement dual-search read-path fallback in LocalFileService
11292 Bump GitHub Actions workflows from node-version 22 to 24
11283 Preserve required lifecycle fields in MetadataManager.save
11281 Preserve archive planning metadata in MetadataManager
11273 Atomic PR review create via dedicated github-workflow MCP tool — close formal-state gap
11267 Cross-family corrective-authorship rotation and FAIR split discipline
11275 Machine-readable skill capability manifest + CI lint enforcement
10118 create-skill: require downstream skill-manifest updates
11128 peer-role-mode.md: codify pro-active essential + session-sunset duration (sister to #11124)
11270 Fix pre-flight skill discovery and create-skill checklist drift
11268 Skill-substrate-cleanup: Map→Atlas relocation for 3 over-floor SKILL.md routers (session-sunset, lead-role, peer-role)
10658 Fix Claude bridge prompt-focus regression
11254 [Epic] Institutionalize Architectural Pre-Flight Skills
11235 Add source-ticket currency gate to pr-review
11107 Move toolService.mjs files back to MCP server directories (M6 retrospective architectural fix)
8891 Restore Buffered Grid Stability
8892 Create Component Test for Grid Teleportation Artifacts
11233 Extend create_issue MCP tool with ProjectV2 membership API support + retire release:v13 label hack
11224 Migrate memory-core services to flatter SDK structure (M6 MC)
11241 Implement 3-Layered "Helpful Assistant" Regression Drift Defense (Discussion #11238 graduation)
11243 Extend peer-role-mode.md with schlagfertig-discipline + discipline-dressed-deference anti-pattern
11236 Strengthen ideation-sandbox graduation→closure: RESOLVED_TO_AC scope clarity + compliance-detection guard
10961 Pilot GitHub Projects for v13 — derived release-focus view
11022 Orchestrator decomposition (M3.5): extract ProcessSupervisorService, TaskStateService, CadenceEngine
10822 Config substrate cleanup: KISS hard cuts + three-tier model
10733 Coordinated cognitive-load audit: AGENTS.md + boot ramp + skill manuals (post-#10429 successor)
10924 Bucket G: additional unit-test substrate failures discovered post-#10903 Phase 2
11229 Fix epic-resolution-workflow.md §4 misread: epic-close ≠ PR-merge §0 invariant parallel
10691 Shared KB/MC Team Deployment MVP
11209 Graduate Discussion #11206 Option A-prime — refined lead/peer-role coordination protocol
11204 Harden test harness mocking for dynamic ESM imports
11221 Close §15.6 "OR state your intended next lane" loophole — announce AND execute
11218 Implement 4-Tier Decision Escalation Ladder to Eliminate "Helpful Assistant" Regression Drift
11195 Validate Step 2.5 Architectural Step-Back post-merge (30-day observation)
11217 Consensus mandate for ideation-sandbox graduation + PR-merge gate
11213 Session Sunset Protocol: Agent-Level vs Swarm-Level Split
11205 lead-role-mode.md: mandate explicit /peer-role skill-trigger naming in A2A messages
11211 Session Sunset Protocol: Agent-Level vs Swarm-Level Split
11198 IssueService archive-write path refactor for lazy ordinal chunking (#11187 AC3)
11202 Backfill hasCoreSwarmParticipant misses 33 sessions with non-shared userId
11201 Fix HealthService backup.error: fs.readdir is not a function
11003 Implement Dockerized remote MCP transport proof (v13 Release Gate)
11197 DiscussionService flat active-tier and lazy ordinal archive refactor (#11187 AC5)
11196 PullRequestService archive-write path refactor for lazy ordinal chunking (#11187 AC4)
11190 Add archivePath helper for sealed archive chunks
11189 Phase 1: Refactor Config for Archive Shape Management
11192 Graduate Step 2.5 Architectural Step-Back from Discussion #11188
11181 Restore shared summary visibility for swarm identities
11185 Detect stale magic-close keywords in PR commit bodies
8890 Fix VDOM Update Collision Logic for Sparse Trees (Teleportation)
11169 Add operator-local config for orchestrator dev-sync roots
11177 Persist active-PR-cycle-state in sandman_handoff for nightshift boots
10946 DreamServiceGoldenPath.spec:77 residual flake post-#10940 engine='hybrid' fix
11165 post-review-pickup §4 criterion #1 condones deference-slip — revise to mandate backlog self-select + announce
11163 bootstrapWorktree: generate dist/parse5.mjs (+ minimal build artifacts) so worktree can run full unit suite
11154 Extend §7.4 Rhetorical-Drift Audit to cross-PR reviewer-seeded drift
11121 Migrate PR conversations data to hierarchical chunking (XXxx)
11135 Configure dev auto-sync for multiple repo clones
11161 Migrate knowledge-base services to SDK (M6 Tier-1)
10935 TransportService.spec:23 still flakes after #10930 bind-race fix — second race surface
10936 G5#2: KBRecorderService.spec singleton-data pollution under workers:1
10941 G5#5: GraphService.spec:107 residual flake post-TestLifecycleHelper migration under workers:1
11160 Lead-role end-of-turn Pre-Flight reasoning-statement + anti-deference anti-patterns
11155 Restore github-workflow projectRoot to v12.1.0 cwd-primary shape (revert #11149)
10934 FileSystemIngestor.spec flakes on shared GraphService SQLite-close under workers:1
10942 PullRequestService.spec:250 flake — getPullRequestDiff file parameter filter under workers:1
10983 Migrate knowledge-base services to flatter SDK structure (M6 KB)
11156 Generalize Worktree Bootstrap Protocol to Antigravity
10938 G6: Database.spec did-not-run — SQLite.initSchema closed-db reuse under workers:1
11152 Hardening GitHub Workflow pathing and documentation
11147 Fix github-workflow MCP config projectRoot pathing resolution
11150 Harden production-scale ai:restore path: Neo bootstrap + chunked Chroma upsert + streaming validateBundle
11141 Enhance ai:restore merge mode: preserve-live INSERT OR IGNORE semantics + label-filter + per-substrate targeting + post-restore hooks
11145 Reject sync_all MCP tool when caller's working tree is not on dev branch
11148 Reject sync_all MCP tool when caller's working tree is not on dev branch
11140 Patch Store.clear() cascade bypass of destructive operation guards in SQLite.removeNodes
11136 A2A peer-engagement: name skills literally in routing requests (e.g., /pr-review on PR #N)
11138 fix(github-workflow): LocalFileService.getIssueById missed chunkPath in active-issue read path
11017 Orchestrator task: primary-checkout `dev` auto-sync + KB cascade
11126 feature(github-workflow): Implement write-path chunking for IssueSyncer
11124 lead-role-mode.md: codify session-sunset duration + positive-framed lane-coordination pattern
11118 Chunk resources/content/discussions/ to bypass GitHub's 1000-file folder cap (preventive sibling to #11113)
11131 Integrate PR sync script into release publish workflow
11134 enhancement: mitigate systemic friction from interleaving chore-sync commits on active branches
11117 Chunk resources/content/pulls/ to bypass GitHub's 1000-file folder cap (sibling to #11113)
11074 Extract WakeSubstrateCoordinatorService as M4 per-task coordinator (fold bridge-daemon into orchestrator)
11073 Extract HeartbeatCoordinatorService as M4 per-task coordinator (fold SwarmHeartbeatService into orchestrator)
11065 Extract SandmanCoordinatorService as M4 per-task coordinator (orchestrator-driven Sandman/DreamService scheduling)
11113 Subdivide issue directories to bypass GitHub's 1000-item folder limit
11108 Remove window duration telemetry from A2A wake messages
11105 pull-request skill: add author-side check that reviewers use correct pr-review template
11103 github-workflow MCP boot fails: toolService.mjs has stale 3-dot relative import (post-#10997 M6 migration)
11077 M4 Architectural Convergence: Orchestrator Supervision & Unified Daemons
11094 Event-Driven Issue Sync and Golden Path Synthesis
11099 Compress Double Diamond skill rules into Atlas payloads
11092 AGENTS.md core-value triggers: friction→gold §13.X + V-B-A §3.5
11093 Migrate Daemon Supervision to AgentOrchestrator
11086 Add Double Diamond graduation guard to ideation-sandbox
11090 Compress new skill rules into Atlas payloads
11081 Rename Orchestrator.mjs to AgentOrchestrator.mjs
11080 Orchestrator daemon fails to start (Sub-4 #11064 regression)
11084 pr-review skill: Cycle-1 premise pre-flight + Drop+Supersede framing triggers
11082 Implement Double Diamond guard in Ideation Sandbox
11078 Enforce Double Diamond divergence guard in ideation-sandbox
11072 Extract GraphMaintenanceCoordinatorService as M4 per-task coordinator (Hebbian decay + GC scheduling)
11071 Extract GoldenPathCoordinatorService as M4 per-task coordinator (Golden Path synthesis scheduling)
11070 Extract DreamCoordinatorService as M4 per-task coordinator (DreamService cycle scheduling)
11062 Extract BackupCoordinatorService as M4 per-task coordinator (orchestrator daily backup)
11068 M3.5 Sub-4: Orchestrator slim-down + TaskDefinitions extraction
10937 G5#3: PermissionService.spec AGENT:* singleton cross-pollution under workers:1
11066 bridge-daemon launchd/systemd packaging (close operator's bridge terminal)
10780 Codify backup-first operational discipline before DreamMode/Sandman invocation
11058 Split SwarmHeartbeatService into class file + ai/scripts/ entry-point wrapper (Orchestrator pattern)
11057 Abstract fixture identities in team/private retrieval spec
11051 [ai] Extract CadenceEngine from Orchestrator (M3.5 Sub-3)
10951 Add team-private retrieval integration tests for Memory Core
11049 ai/ Neo namespace bootstrap hygiene: entry-point-only Neo+core+InstanceManager imports
11050 [ai] Refine Lead/Peer Role Exit Conditions to Align with Session Sunset
11052 [ai] Update lead/peer role SKILL.md to reflect session-sunset exit conditions
11031 Create /peer-role skill — SKILL.md + reference payload + AGENTS.md §21 row (graduates Discussion #11026)
11038 Implement Autonomous Swarm Lead Rotation (A2A Baton Pass)
11019 v13-path.md substrate update: D3 scope additions for backup, FS ingestor, cadence design, MX metrics
11046 [Bug] Verify ai:syncKnowledgeBase.mjs behavior
11029 Add per-recipient read receipts for A2A broadcasts
11039 Extract TaskStateService to isolate state-mutation API
11030 Add AGENTS.md §15.6 Swarm Topology Anchor — Flat Peer-Team Model (graduates Discussion #11026 OQ4)
11027 Codify "contributions over commits" in AGENTS.md §13 + Atlas qualitative measurement framework
11028 Create /lead-role skill — SKILL.md + reference payload + AGENTS.md §21 row (graduates Discussion #11024)
11032 [Skill Enhancement] Enforce assignee check in pull-request Pre-Flight to mitigate 30% unassigned closure rate
11018 Orchestrator owns daily backup with 30-rotation retention
11020 gh-workflow sync: skip NOT_PLANNED snapshots + on-release archival automation
11013 Surface primary-checkout `dev` staleness in session-sunset
11009 Move Orchestrator logic into Neo daemon class
10009 Playwright Test Coverage: Federated Cloud Topology
11011 Retire chromaUnified flag + federated Chroma topology
10990 Defer federated mode topology deployment coverage
10449 structural-pre-flight skill: implementation + Phase 1 adoption
10986 Migrate Tier-1 MCP services to flat SDK boundary
11005 Align Neo classNames with flat SDK locations (M6 follow-up sweep)
11006 Move summary and KB sync triggers into orchestrator MVP
10996 Migrate memory-core services + managers to flat SDK boundary
8867 feat: Implement incremental updates for Card Layouts
8869 Fix: VDomUpdate merged updates do not support recursion
8873 Refactor: Standardize VNodeUtil and VDomUtil getChildIds to include components
8874 Investigate addVnodeComponentReferences Data Loss & TreeBuilder Symmetry
10969 Document deploy compose env-var toggles
10994 Migrate neural-link services to flat SDK boundary
10993 Migrate github-workflow services to flat SDK boundary
10991 Migrate knowledge-base services to flat SDK boundary
10970 Codify post-review immediate next-phase pickup discipline
10987 Replace Claude Space wake seed with r undo sequence
10947 Add real OIDC auth integration fixture for Memory Core
10949 Prove backup restore and wipe detection for deployed Memory Core
10813 Restore session summaries: primary-flag gate + sunset-event trigger
10965 MCP server common base class with standardized extension points
10980 Document MCP server BaseServer extension contract
10971 Harden daemon summarization single-writer semantics against crash-restarts
10972 Complete NEO_MC_PRIMARY retirement from Memory Core
10964 Harden clean-checkout AI deploy bootstrap
10956 Migrate Memory Core summary sweeps to daemon
10952 Audit Memory Core integration CI skip gates
10939 Re-add unit matrix row to test.yml — gated on TestLifecycleHelper substrate stabilization
10957 Document v13 architectural path — slim MCP servers, orchestrator daemon, SDK migration sequence
10944 Remove stale sqlite-vec artifacts from Memory Core healthcheck
10932 TransportService.setup() races Express bind — fetch fires before listener accepts
10783 Healthcheck observability: features.wake block (gate-state + daemon-running-state + last-pulse timestamp)
10931 Track POLL_INTERVAL env var in features.wake stale-threshold
10917 CrossTenantIsolation integration spec: alice add_memory returns isError post-substrate-fix
10923 CoalescingEngineService.setMcpServer regression: rename in #10916 left dangling test consumers
10903 Audit unit-test failures in clean CI env (substrate-data + browser gaps)
10918 HeartbeatPropagation uptime equality: consecutive samples report identical process.uptime() values
10897 CI workflow: matrix(unit, integration) test runner
10915 MCP servers fail in deployed CI: singleton-transport reconnect + auth env var mismatch
10913 Chroma healthcheck times out: needs start_period for cold-start grace on CI
10911 Chroma healthcheck still fails: `python` binary not in PATH (chromadb slim image uses `python3`)
10908 Chroma healthcheck fails in CI: chromadb/chroma image lacks curl
10896 Sustained-liveness helper + heartbeat propagation integration spec
10905 Institutionalize CI / Security Checks Audit in PR Review Skill
10895 Identity fixture + tenant isolation + auth-rejection integration specs
10902 Dockerfile npm ci fails: prepare lifecycle needs buildScripts before COPY
10889 Relocate buildScripts/ai test specs to right-hemisphere unit-test root
10815 initServerConfigs: detect template drift, refresh stale config.mjs
10841 Enrich manage_discussion_comment with commentId payload
10805 Build staged-stack integration test harness for shared cloud deployment
10887 Institutionalize Test Location Audit in PR Review and Pre-Flight Skills
10871 Backup/restore parity: enhance ai:backup + new ai:restore
10884 Fix stale MC model env vars in SessionService specs
10801 Create reference Docker and docker-compose artifacts for shared KB/MC deployment
10882 Mitigate Completion Bias in Sunset Protocol
10878 Update Authorization.spec.mjs env-var fixtures post-#10877 NEO_ rename
10881 Authorization.spec.mjs: resolve listener watches wrong stream (stdout vs stderr)
10862 Prefix Neo-specific env vars with NEO_ across MC, KB, Tier 1 configs
10796 pr-review skill §2.7 missing formal-review-state step — substantive review comment ≠ cross-family Approve gate
10843 Extract shared BaseConfig for MCP Servers
10844 Daily automated snapshot pipeline for Memory Core data substrate
10845 Block destructive AI substrate ops on production paths
10869 Mandate A2A notifications for ANY lifecycle event in AGENTS.md
10867 Mock Memory Core Chroma collections in Playwright unit tests
10864 Document Codex mid-session harness restart recovery
10842 Substrate Config Refactor: applyEnv Priority Inversion Fix
10721 Shared deployment MVP completeness gaps (post-#10691)
10774 Document trustProxyIdentity threat model + operator config in SharedDeployment.md
10834 Trim sync_all tool description to comply with 1024-char limit
10856 Native Edge Graph SQLite: enable PRAGMA foreign_keys=ON for cascade integrity
10835 Cross-link PR branch-constraint in pull-request-workflow.md
10860 Optional per-agent GitHub credentials: operator-supplied identity→token mapping
10855 Epic priority-0 mechanical gate: block sub-issue creation until parent's P0 ACs clear
10857 Active operator-constraints feed: cross-session mandate propagation primitive
10854 Memory Core wipe-detection alarm: collection-count-delta substrate primitive
10859 Per-domain env-file split: replace monolithic .env with .env.<domain> substrate
10858 Per-agent credential namespacing: replace shared GH_TOKEN with identity-scoped variables
10825 Audit dead config fields for substrate cleanup
10847 Enforce test environment isolation by reinstating testing triggers in AGENTS.md
10824 Audit MCP env vars for config substrate cleanup
10827 Create top-level ai/config.template.mjs shared globals (Tier 1 NEW)
10838 Refactor Neo.isEmpty() internally and adopt it in EmbeddingProviderConfig
10823 Config Cleanup: Delete legacy env-var aliases (Phase 1)
10830 Update sync_all tool description to enforce dev branch constraint
10826 Codify clean-slate sunset rule in pull-request-workflow §1.1
10820 Enable Codex sandbox network in template
10803 Publish reference reverse proxy config for shared topology
10802 Expose public canonical URL configuration to MCP servers for SSE and OAuth callbacks
10808 Operator-facing env var ergonomics: descriptive names + Chroma host/port overrides
10804 Consolidate neoEmbeddingProvider and chromaEmbeddingProvider configurations
10800 Author cloud deployment cookbook for shared KB+MC topology
10773 Healthcheck observability: providers.neoEmbedding (SQLite-side, symmetric to providers.embedding)
10770 Healthcheck observability: providers.auth block (symmetric to providers.embedding)
10772 Unit test coverage for proxy-identity injection in TransportService
10765 Mutation-time substrate gate (pull-request Pre-Flight + AGENTS.md §13)
10786 Test isolation bug: harnessLifecycle.spec.mjs fails under default-worker config (shared state-file identity)
10789 Implement SwarmHeartbeatService as Neo-singleton in ai/daemons/ (replaces bash-shape #10781 attempt)
10794 Refine substrate-mutation gate (learn/agentos carve-out + reviewer enforcement)
10787 Add daemon-only entrypoint to swarm-heartbeat.sh (split heartbeat from agent-CLI launcher)
10781 Persistent-process management for swarm-heartbeat.sh daemon (#10671 epic-finish piece)
10761 Codify blocked task-state coordination
10784 PR #10782 doc follow-ups: slot-rule retrofit + AGENTS_STARTUP §9 + pull-request driver-mode cross-link
10671 Substrate-restart recovery (two-mode: idle-out + sunset)
10399 Swarm Stall: Mutual Idle State without Heartbeat Mitigation
10396 Implement heartbeat wakeup to prevent swarm stall on mutual idle
10777 Agent-runtime engagement discipline (V6: triage-not-engage default + leased-driver continuity)
10775 Mechanical Pre-Flight: enforce evaluation-metrics block in pr-review comments
10724 Local chat-API summary provider validation
10723 Local embedding provider validation
10727 Deployment-target OAuth2.1 / X-PREFERRED-USERNAME integration
10766 Periodic substrate-audit primitive + leased-driver heartbeat recovery
10760 Slot rule + disposition taxonomy + byte budget retrofit into create-skill authoring guide
10756 Empirical grounding for §8 / §7.2 cross-model asymmetry codifications
9958 System Prompt Token Optimization via Mermaid Graphs
10753 Update Co-Authored-By git trailer mapping to use canonical @neomjs.com email addresses
10738 Asset template audit: anchor-preserving first-pass vs follow-up split
10736 Boot-ramp split: replace CodebaseOverview Step-1 mandate with README + Architecture.md
10748 Extend get_pull_request_diff with per-file + SHA-pinned scoping
10749 Standardize Triad Swarm Git Email Domains to @neomjs.com
10737 Skill payload audit: extend #10537 methodology to remaining workflow manuals
10734 Baseline & inventory: per-harness loaded-surface measurement methodology
10742 Compress restored AGENTS.md paradigms without losing anchors
10743 Compress §13 + §15.5 prose density (anchor-preserving)
10740 Restore over-extracted anti-drift paradigms post-#10735 compaction
10735 AGENTS.md compaction with 3-axis slot rule and net-deletion budget
10725 Resume tool / session-handoff surface
10726 Disconnect-triggered summarization wiring
10722 Per-session purge MCP tool
10715 Route Codex reference notes into Codex-only turn context
10704 Implement Contract Completeness Gate and Contract Ledger
10083 [meta] Soften AGENTS.md §9 "Single Full-Read Rule" framing for frontier-context-era models (preserve efficiency guidance)
10717 Wake subscription API hides stale active rows that bridge still dispatches
10694 Shared KB/MC deployment profile and validation
10693 Summarization coordinator for shared Memory Core
10708 Update pr-review skill to audit Contract Ledger
10707 Update ticket-intake skill to verify Contract Ledger
10706 Update ticket-create skill to mandate Contract Ledger
10705 Author contract-ledger.md taxonomy documentation
10692 Client-scoped Memory Core session lifecycle
10668 Suppress self-wakes for AGENT:* broadcasts
10714 Codex sandbox bootstrap probe for .neo-ai-data/sqlite access
10679 Codex Desktop terminal-restart + prompt-injection mechanism investigation
10677 Claude Desktop terminal-restart + prompt-injection mechanism investigation
10698 Epic-resolution skill + Substrate Evidence Ladder graduation (Discussion #10697)
10676 Sunset-mode restart substrate with fail-closed gate and verify-effect ACs
10678 Antigravity terminal-restart + prompt-injection mechanism investigation
10672 Forensic record: 2026-05-03 runaway-spawn pattern (root cause + timeline)
10675 Idle-out A2A in-place nudge with cooldown + no-spawn invariant
10673 checkSunsetted detector contract: emit sunset vs idle_out_candidate signals
10674 In-flight boot/restart lock primitive (identity-uniqueness mutex)
10686 Test Isolation: Environment-based OpenAPI injection to prevent parallel test interference
10681 Mock osascript in resumeHarness/bridge-daemon unit tests (host-environment side-effect bug)
10666 Stabilize Codex r focus seed cleanup and metadata support
10664 Fail closed for Codex UI wake after Space seed failure
10647 Stabilize A2A wakeups before heartbeat reactivation
10662 Add Codex focus seed default to bridge-daemon (mirrors #10661)
10660 Add Claude bridge Space focus seed
10643 checkSunsetted ORDER BY picks legacy rows for originSessionId extraction
10650 Codify wake restart and incident protocol
10649 Add cross-harness wake prompt-landing matrix
10645 AgentIdentity cache miss breaks wake bootstrap templates
10601 Auto-wakeup substrate for sunsetted agents (recovery layer)
10644 Antigravity Cmd+L wake-delivery falls through to vscode file write
10648 Add wake reactivation gate and circuit breaker
10651 Use raw memories for recent memory-mining freshness
10646 Require live open-queue sweep in ticket-create
10636 Wake subscription validAppNames omits Codex, breaks @neo-gpt bootstrap
10641 checkSunsetted false-positive on stale memory spawns orphan sessions
10638 Capture osascript stderr in bridge-daemon.mjs
10626 Cooldown-bounded idempotent trio wake (binds to all-agent-idle detector contract)
10625 All-agent-idle detection at heartbeat layer (substrate primitive for trio liveness)
10624 Wake subscription canonicalization: one canonical appName per identity, retire stale duplicate
10617 Close residual drifts in pr-review §9 / §9.1 substrate (#10615 follow-up)
10620 Normalize AGENT_MEMORY nodes to use structured timestamp and sessionId columns
10622 Auto-wake heartbeat skips every pulse: get_unread_count uses wrong JSON path ($.type vs $.label)
10611 Auto-Wakeup substrate semantic correction: fresh-session-spawn + boot-grounding prompt
10614 pr-review compression Sub 2: Pilot extraction (§5.3 MCP-Tool-Description Budget)
10540 pr-review compression Sub 1: Loaded-surface measurement methodology + baseline
10615 Codify reviewer step-back patterns + surface author Reject-with-Rationale
10609 Cross-reference Pre-Decision Sunset Gate ↔ session-sunset workflow ↔ #10601 recovery substrate
8755 Enhance LivePreview to Support Mermaid Diagrams
10606 resumeHarness cooldown path: use __dirname-based resolution, not process.cwd()
10599 Reduce Heartbeat Concurrency Lock TTL to 10 Minutes
10081 [enhancement] ask_knowledge_base query telemetry — Agent FAQ signal for gap inference
10604 Implement Harness Registry and fresh session terminal booting
10030 [Epic] Concept Ontology & Semantic Gap Inference
10319 chore(ai): define and implement heartbeat concurrency semantics
10595 sweepExpiredTasks.mjs direct-invocation fails with "Neo is not defined"
10564 Investigate Gemini-specific premature sunset trigger drift (7th+ occurrence)
10080 [enhancement] Relevance-bounded query APIs for ConceptService — prevent context window flooding as ontology grows
10318 chore(ai): empirical token-economy anchor for swarm heartbeat
10591 Cross-clone symlink for sandman_handoff.md in bootstrapWorktree
10586 AGENTS_STARTUP.md §6 boot-summarization claim is silently false
10037 ChromaDB Concept Embedding & Hybrid Search
10587 Capture runSandman inference hard-failures durably
10584 Memory Core + Neural Link: export neoRootDir on defaultConfig for symmetry with KB
10574 Concept nodes: add non-destructive verifiedAt freshness
10582 logger symmetry: extend always-on file sink to Memory Core and Neural Link MCP servers
10460 DreamService marks graphDigested:true on partial MemorySessionIngestor failures
10576 KB sync observability: tee MCP child logger output to .neo-ai-data/logs/ for tail-able progress
10579 KB Sync: Implement stderr observability (Shape A)
10577 Bridge Daemon: Serialize osascript execution to prevent concurrent injection collisions
10572 VectorService.embed: branch on chunksToProcess.length to prevent agent freeze on bulk resync
10434 list_messages status:'unread' filter misses messages with readAt:null
10456 chore(docs): audit and update README with real LOC metrics (The Million-Line Organism)
10088 [enhancement] Automate post-merge knowledge-base sync trigger
10461 Chunk getDeltaLog IN-clause to avoid SQLite parameter overflow
10469 Codify Verify-Before-Assert Pre-Flight Check in AGENTS.md core directives
10555 Codify ticket reality classification in ticket-intake
10569 Restore Memory Core boot-time auto-summarization (startup.summarizationStatus = not_attempted)
10556 Memory Core ChromaDB: backfill legacy userId for tenant-aware reads
10559 Guard MCP config template changes in PR workflows
10560 pr-review skill: router-level template pointers (Cycle 1 + Cycle N)
10562 Enhance System Prompt Firewall: Institutionalize Digital Organism Identity
10557 Memory Core: guard StorageRouter against non-iterable strategicNeighbors
10003 Standardize Global Vector Embedding Configuration
10545 Tighten wakeSuppressed description in add_message MCP tool
10538 Codify cross-reviewer divergence in PR Review Routing Protocol
10531 Preserve MCP defaults, bounds, and choice enums
10552 Make Codex project instructions load deterministically
10550 Harden Antigravity System Prompt Firewall using XML tags
10548 Institutionalize Antigravity MX Negative Override
10543 Implement Phase 2 Session Sunset Protocol (Unsubscribe Primitive)
10535 Formalize Swarm PR Review Routing Protocol in pull-request skill
9671 Neo AI Architecture Masterplan (Antigravity & Agent SDK)
10504 Fix CollectionProxy undefined collection crashes and config key mismatch
10407 Bug: manage_wake_subscription Zod schema silently strips harnessTargetMetadata extension fields
10525 Surface wake priority and defer non-high interrupts
10529 Disambiguate session sunset triggers from PR review halting
10527 Support JSON Schema enums in MCP tool inputs
10499 ChromaDB multiple operator query error in MemoryCore
10523 Generalize Resumption Protocol to A2A interrupts
10521 Architecture: Codify Anti-Rubber-Stamp PR Defense Protocol (Extract Review Response)
10439 Document wake-substrate auto-bootstrap in AGENTS_STARTUP.md (defense-in-depth)
10518 Remove manual wake subscription sequence from agent startup
10506 Shrink manage_database MCP tool description to respect agent reasoning budget
10509 Mandate State Verification in PR Review Context Initialization
10515 Stabilize A2A Wake Substrate Integrity
10442 manage_wake_subscription update action: overwrite-vs-merge semantics on harnessTargetMetadata
10452 Identity Rewrite: Neo as a Self-Evolving Digital Organism
10513 Add delta re-review template for PR review cycles
10501 Enforce empirical checkout mandate in PR review protocol
10511 docs(agents): compact AGENTS.md to restore turn-based memory focus, and streamline PR skills
10488 Overcome Codex Desktop Context Window Limits for Marathon Sessions
10498 Prevent sunset self-DMs from waking active sessions
10496 Add skill trigger pre-flight for prompts and A2A
10492 Add Codex (GPT) to the Swarm maintainers table in README
10489 Unify Agent Skills Directory to `.agents` Standard
10450 Mandate formal closure of GitHub Discussions upon Epic graduation
10458 Implement Manual Session Summarization CLI Script
10485 Add Codex Desktop harness support
10474 Harden §0 invariant against mechanical and semantic loopholes
10472 Phase B: Verify-Before-Assert Tool Inventory & Cross-Skill Integration
10484 Fix LM Studio Monolithic JSON Payload Crash & Refactor SQLite Batch Size
10478 Seed Agent Identity for Codex (GPT-5.5) in Memory Graph
10294 P6b: MCP Middleware Guards — structured policy config enforces tenets at tool boundaries
10443 Bridge daemon's `meta.appName || 'Claude'` silent fallback masks sub-config bugs
10470 Codify Verify-Before-Assert Pre-Flight Check in AGENTS.md core directives
10467 Bridge daemon wake delivery keystroke-injects into VS Code active editor
10465 Bug: Bridge Daemon hits SQLite parameter limit in standalone queries
10463 Bug: Memory Core SQLite hits parameter limit during massive GraphLog syncs
10424 SQLite WAKE messages invisible to Memory Core MCP API
10444 Fix OSAScript target process resolution for Antigravity (Electron)
10440 Gemini's identity-root template has wrong appName ('Cursor' vs 'Antigravity')
10437 Auto-invoke wake subscription bootstrap on MCP server boot
10435 bootstrapWorktree: support independent-clone canonical via --canonical-root
10432 bootstrapWorktree --link-data: granular per-subdir symlinking
10428 Implement reviewer-side audit for PR keyword syntax in pr-review-guide.md
10426 Support @me addressing in MailboxService and mandate exact PR close syntax
10430 Wake Substrate: enforce duplicate-wake deduplication in coalescing window
10419 Persist bridge-daemon stdout to disk for wake-failure diagnostics
10217 Add PR reviewer-request MCP tool surface
10422 Fix AppleScript UI scripting focus steal bleed in Wake Substrate
10216 Maintainer-side label triage workflow for contributor tickets
10215 Codify 7-day reassignment rule in ticket-intake §3a
10214 Agent operational hygiene: assignment protocols, labels, and inbound channels
10218 Enrich github-workflow healthcheck with notificationPreview
10410 Wake Substrate post-#10404 hardening: idempotency + duplicate deduplication
10395 Antigravity Wake Delivery: Clipboard injection appends to active user input
10414 Wake Substrate Post-#10404 Hardening: Idempotency & Dedup
10408 Wake-trigger sub-variant for AGENTS.md §22 mailbox-check (Interrupt vs Polling)
10405 Enhance PR Workflow to Mandate A2A Notifications for Core Swarm
10402 Bootstrap wake subscription from identity template at session start
10400 Tech Debt: Remove `rawDelivery` bypass once IDE supports `wake/digest`
10301 feat(skills): introduce rhetorical-drift audit to pr-review Depth Floor
10383 Add turn-start mailbox-check Pre-Flight to AGENTS.md
10380 Codify sibling-file-lift discipline in per-turn AGENTS.md
10388 Wire pump() through coalescing engine for Shape A throttle
10357 [Epic] Phase 3: Cross-harness autonomous wake substrate
10393 Unify Bridge Daemon Workspace Runners
10391 Finalize Phase 3 Wake Substrate with Bidirectional Delivery
10389 Boot Crash: WakeSubscriptionService.setMcpServer throws TypeError on null GraphService.db
10358 [Phase 3] Implement Shape A: MCP Notifications Path
10384 TypeError: Neo.setupClass is not a function in full suite Playwright runs
10385 Codify peer-escalation discipline in AGENTS.md (§10.7)
10362 [Phase 3] Token-Economy Throttle (Coalescing Window)
10364 [Phase 3] Anthropic FR: Native MCP Notification Subscription
10361 [Phase 3] WAKE_SUBSCRIPTION Schema and Tool Surface
10363 [Phase 3] Heartbeat-Bypass Detection
10360 [Phase 3] Implement Shape C: Bridge Daemon Fallback
10359 [Phase 3] Implement Shape B: A2A Webhook Push Notifications
10376 Strengthen A2A commentId hand-off discipline (reflex + cold-cache exception)
10374 Refine "Session Sunset" trigger definitions to prevent premature protocol execution
10370 Formalize the Agent Session Sunset Protocol as a Progressive Disclosure Skill
10372 Protocol Enhancement: Codify Pipeline Authority & Forkability Model in AGENTS.md
10368 Refactor AGENTS.md §15 to resolve Knowledge Base tool hierarchy conflict
10367 Resolve tool hierarchy conflict in AGENTS_STARTUP.md
10365 Restructure AGENTS.md / AGENTS_STARTUP.md: critical-gates promotion + per-turn migration + skills awareness + forkability
10355 Draft ADR 0002: Phase 3 wake-substrate standards alignment
10332 Per-turn mini-summaries: short-term-recall substrate for "what just happened" queries
10351 bootstrapWorktree: add npm install step + optional `--build-all` for SDK/test-ready worktrees
10347 Investigate intermittent SENT_TO edge cull on Antigravity-side A2A messages
10339 Track 2C: TTL/Expired sweeper — cron-driven stale-task transition to Expired state
10341 pr-review: codify MCP-tool-description budget audit on OpenAPI YAML
10338 Track 2B: A2A_TASK state-machine + transition authority + idempotency claim-and-lock
10344 Remove Visible Proposal Protocol from ticket-create skill to unblock autonomous creation
10343 Add Resumption Protocol to AGENTS.md to prevent Interruption Amnesia
10334 Transition MailboxService to structured JSON intent payloads for A2A handoffs
10336 ideation-sandbox: codify external-precedent web_search step before Discussion authoring
10333 Implement since_comment_id and comment_id parameters for get_conversation
10330 Single-canonical identity format: purge AGENT:<bare-name> pollution, rename test fixtures, simplify normalizer
10207 docs(skills): promote rebase and base-branch verification in pull-request skill
10310 feat(memory-core): Implement sharedEntity flag for Graph Node RLS bypass
10327 Bug: Edit/Write MCP tools fail silently against .agent/skills/ directory
10324 pr-review must flag PRs that name an epic as close-target — epics close only when all subs resolved
10323 [Epic] Cloud-Native Knowledge & Multi-Tenant Memory Core (reopened from #9999)
10321 Author release-workflow agent skill (deferred until v12.2 ships)
10307 Refactor ai/services.mjs eager-aggregator to support resilient MCP loading
10312 Implement Sleep-Cycle MVP (Heartbeat Cron and Handoff Trap)
10316 Convert absolute skill paths to workspace-relative to prevent antigravity ide hiccups
10314 Fix Claude Code Skills Directory Synchronization
10302 feat(skills): introduce Provenance Audit for major abstractions in pr-review
10283 Extend Pre-Authoring Adjacency Sweep to Meta-Skills (create-skill)
10305 Memory Core MCP Server boot crash due to openapi.yaml indentation syntax
10304 Enrich manage_discussion_comment with Comment-ID hand-off protocol
10272 Comment-ID-aware PR workflow: return IDs on write, selective-fetch params, A2A propagation
10281 Refactor ideation-sandbox skill to adhere to Progressive Disclosure
10273 pr-review scoring: decile anchor rubric with word-per-tier + score-second template order
10299 feat(skills): refine industry-friction-radar terminology (SOTA vs Frontier)
10274 Tighten merge-authorization mandate to require explicit human sign-off
10297 Create `industry-friction-radar` skill
10288 Backtick-escape `#N` references to prevent phantom GitHub auto-links in skill docs
10285 Implement Asymmetric sync_all (Push on dev only)
10278 ideation-sandbox: formalize iterative review-and-graduation workflow for maturing Discussions to epic-ready state
10276 ideation-sandbox: add pre-authoring adjacency sweep to prevent proposal-idea duplication
10275 Cross-session auto-trigger daemon to surface forgotten threads without human prompting
10271 System Node Fragility: Stamp Global Nodes with userId: null
10127 HealthService: surface effective unified/federated topology in /health
10247 Formalize Empirical Isolation Test After Review pattern
10245 docs(ai): add isolation-test-after-review pattern to PR review skills
10244 docs(ai): extend MemoryCoreMcpAuth.md Troubleshooting with identity race failure mode
10255 Per-agent blocking in open reply policy must override default-open (#10253 follow-up)
10256 PermissionService.spec.mjs — fix two pre-existing failing tests on dev
10017 Migration & Backward Compatibility for Multi-Tenant Schema
10267 github-workflow MCP: sync-metadata.json timestamp pushed on no-content-change boot-sync
10260 syncCache must invalidate vicinity of both endpoints when invalidating edges (#10258 follow-up)
10259 Identity normalization — merge aliased AgentIdentity nodes + purge test-fixture leakage + @@ -prefix strip
10257 MailboxService read paths must consume WAL delta before iterating in-memory edges
10240 Claude Desktop onboarding + multi-harness symlink convention in AI_QUICK_START
10252 Mailbox reply policy: config-gated default for deployment-tier selection
10251 A2A Substrate: Transition Mailbox to Opt-Out (Blocklist) Model
10249 bindAgentIdentity drops return value — GraphService.getNode Promise is not awaited (#10241 follow-up)
10248 Document Fresh MCP Client Isolation Strategy for cache bypass
10241 Investigate bindAgentIdentity boot-time race — node-visible-at-61s-unbound-at-3s
10246 docs(ai): add fresh MCP client primitive technique to self-repair skill
10176 Mailbox identity observability + Claude Desktop onboarding docs
10231 PermissionService.grantPermission must not lazy-stub missing targets
10230 upsertNode must lazy-load from SQLite before cache decision
10232 GraphService.initAsync should self-seed AgentIdentity + BroadcastSentinel roots on boot
10238 Extract and prepare swarm trajectory dataset for local-model training
10237 Instrument MX graduation criteria — empirical measurement of substrate effectiveness
10233 SQLite.initSchema DROP-on-upgrade is a silent-wipe fallback
10228 Refactor MailboxService and PermissionService tests to use concrete testDbPath
10226 Remove #10182 self-heal band-aid from memory-core Server.mjs
10222 Remove Memory Core Band-Aids and Polish Cache Coherence
10224 Unify .neo-ai-data across worktrees via bootstrap symlink
10179 Mailbox reachable-counterparty skips broadcast receipt path
10190 Implement chosen shared caching substrate for Memory Core
8410 Agent OS: Implement 'Janitor' capability for automated Ticket Sync
10212 Mandate pre-push rebase to close stale-branch hygiene gap under rapid merge tempo
10208 Mandate cross-family PR review; time-bounded self-review fallback
10200 Add regression test for config template round-trip (sync_all)
10188 Add boot-time sibling-PID logging to memory-core Server.mjs
10210 chore(ci): enforce canonical MCP test location via lint/CI rule
10189 ADR for shared caching substrate for Memory Core
10199 diagnoseMcpConcurrency UX polish: Windows fail-fast + per-PID file collection
10191 sync_all crashes with path argument error when multiple clones exist
10195 Antigravity Config Hardening & Cleanup
10187 Diagnose MCP concurrency with lsof/fuser
10192 Implement set_session_id MCP tool and document Handoff Retrieval Hints
10194 Session Continuity Discovery Primitive: Implement get_recent_session_ids
10184 Identity binding stays null post-#10182 — enable debug logging + diagnose
10183 MCP Server Integration Testing Harness for CallToolRequestSchema
10181 Memory-core stdio identity binding non-deterministic after DB re-seed
10149 Mailbox: extend memory-core healthcheck with inbox + outbox preview
10174 Mailbox SENT_TO edges silently culled by linkNodes FK check
10169 Implement TAGGED_CONCEPT auto-emit via SemanticGraphExtractor on message bodies
10168 Expand mailbox test coverage and role-based addressing
10153 Lazy back-fill: Memory + Session nodes for pre-migration Chroma rows
10147 Mailbox: Message node schema + addMessage / listMessages / getMessage / markRead
10146 Cross-tenant permission edges + multi-tenant validation test suite
10145 OAuth2 authentication layer for Memory Core MCP connections
10152 SemanticGraphExtractor: emit typed edges to Memory + Session nodes
10144 AgentIdentity node type + GitHub account binding for model identities
10109 PR comment hygiene — update existing self-review vs. add new comment per lifecycle stage
10141 Extend pull-request skill to enforce model self-identification in PR bodies
10159 Enforce epic-review Execution in ticket-intake Pre-Pickup Validation
10151 DreamService: deterministic ingestion phase for Memory + Session graph nodes
10156 pr-review: add depth-floor mandates to prevent rubber-stamp approvals
10154 Add epic-review skill: vision-fit gate + sub-structure review for new epics
10135 Audit Agent OS for Windows support
10134 Add regression coverage for Memory_DatabaseService#exportGraph newline emission
10132 Retire manage_database_backup MCP tools (backup.mjs replaces them)
10129 Backup: atomic timestamped bundle across all persistent subsystems
10000 Hardened Identity Ingestion & Tenant Isolation
10007 Memory Core: Bypass Database Initialization in Unified Mode
9748 Update ROADMAP.md to reflect v12.2 target (#9999 + #10030 + multi-body grid)
10001 Dynamic Topology: Unified vs. Federated Routing
10104 ticket-create skill — centralize issue creation discipline outside tool descriptions
10113 Reduce DevIndex Spider CI loop from 3x to 1x per pipeline invocation
10112 Propagate GraphQL errors through LabelService instead of returning wrapper objects
10110 Remove commentsTotal sentinel sweep — derive count from timelineItems
10108 Decide me=this policy across the repo — standardize or document the frontend/Node.js boundary
10107 Audit core.Base + Neo.mjs — document rationale, benchmark hot paths, file follow-up refactors only where data supports
10106 ConceptDiscoveryService output schema — add extraction_metadata (missing_fields, ambiguous_references, confidence_score)
10036 Memory Core Concept Discovery & Glossary Enhancement
10086 [enhancement] Promote GUIDE_GAP_WEIGHT_THRESHOLD to aiConfig.data for human tuning
10087 [enhancement] ORPHAN_CONCEPT signal — distinct display channel in sandman_handoff.md
10085 [enhancement] ConceptIngestor follow-ups post-#10035 — hoist concept-graph pass to cycle-scope + dedicated spec + observability polish
10074 [blog] Claude Code × Neo.mjs — what it felt like to realize the organism already existed
10095 [bug] Worktrees fail to bootstrap ai/services.mjs — gitignored config.mjs + symlink namespace collision
10097 [bug] ask_knowledge_base returns empty synthesis for type='src'/'ai-infrastructure' queries despite correct references
10092 [bug] IssueSyncer delta-sync is blind to comment deletions — updatedAt does not bump
10090 [bug] IssueSyncer silently drops content past timelineItems cap — handoff comment on #10030 lost
10089 [docs] Document SQLite FK constraints on Graph Database.addEdge JSDoc
10035 Graph Integration & GapInferenceEngine Refactor
10079 [skill] Broaden ticket-intake's Hypothesis gate to verify written claims against precedent (numerical + architectural + procedural)
10033 Concept Graph Unit Tests
10075 [skill] Add memory-mining skill — formalize the memory-first reflex as a state-transition gate
10072 MCP: list_stores regression — client response shape diverges from OpenAPI declaration
10070 MCP: Open-bag input objects silently stripped — six Neural Link write tools broken since #10043
10068 [docs] Formalize memory-first reflex as per-turn mandate for ticket work
9837 MCP: Output schemas reject responses with extra properties (additionalProperties:false drift)
10057 Knowledge Base: Add PullRequestSource for PR Conversation Embeddings
10064 MCP: OpenApiValidator emits array schemas without items, crashing strict validators (Copilot)
10063 Claude Code hook: auto-persist turn memories via ai/services.mjs (eliminate manual add_memory)
10061 Agent protocol hardening: commit-format Pre-Flight gate, harness branch acceptance, and memory-file mapping
10059 Claude Code harness: auto-load AGENTS.md via .claude/CLAUDE.md + commit shared skills + gitignore worktrees
8288 Neo Agent OS: Orchestration & Swarm Architecture
10058 Memory Core Graph: Add PR Nodes and RESOLVED_BY Edges for Ticket→PR Mapping
10056 Portal App: Add Pull Requests and Discussions to the News Section
10054 chore(ai): add self-review detection to pr-review skill
10051 Enhance Ticket-Intake Skill: Branch-Before-Code Mandate
10049 Concept Schema Enrichment: Aliases, Analogous Edges & Rich Descriptions
10032 ConceptService & Source Code Wiring
10031 JSONL Schema & Concept Seed Extraction
10012 DreamService: Federated Execution Batching & Throttling
10006 DreamService: Semantic Edge Injection into Native Graph
10004 DreamService: Omnidirectional Gap Inference Engine
10002 Universal Macro Overlay DB Topology
10014 [Sub-Epic] Macro Knowledge Base & Semantic Gap Inference
10018 Autonomous Healthcheck Workflow for Frontier Model Agents
10043 Fix MCP OutputSchema Strict JSON-RPC Compliance and Zod Array Type Mapping
10041 Agent OS Failsafes and Anti-Gravity IDE Guardrails
8167 Harden Return Trip Logic for Detached Items
10028 Finalize DreamService Decomposition: Tri-Vector & Topology Extractors
10013 [Sub-Epic] DreamService Decomposition
10023 feat(agentos): Implement Continuous "Tech Debt Radar" via Frontier RAG Sweeps
10022 chore(ai): Eliminate latent architectural debt (vec0, test topology, config)
10021 perf(ai): Eliminate Map-Reduce chunking bottleneck in local inference
8621 Investigation: FocusManager Stability during Atomic Moves
9991 Mirror current workspace snapshot to GitHub
9997 enhancement: Prioritize latest active sessions in summarization pipeline
9993 AI Target: Deprecate Legacy DOC_GAP Inference in DreamService
9952 Sandman Handoff: Top 5 Actionable Tasks Dashboarding
9994 Align Guide Gap Inference with Concepts instead of Files
9992 Refactor Test Gap Detection Logic in DreamService
9903 RLAIF Trajectory Curation & Whitebox E2E Pre-Flight
9986 docs: add "Progressive Disclosure Skills" guide
9985 docs: add "The Dream Pipeline & Golden Path" guide
9983 [Guide] Swarm Intelligence & Autonomous Sub-Agents
9981 [Guide] Agent OS Architecture Overview
9980 Architect MCP Capability Gating by Model Tier
9951 Scaffold signal_state_transition MCP Endpoint
9977 fix: MCP Infrastructure Stability — Stdout Pollution, Crash Recovery, & Triage Mandate
9975 Hardening Agent Intake via Empirical Verification & Historical Domain Querying
9973 Triage Memory Core `summarize_sessions` Token Exhaustion (n_ctx 4096 Error)
9971 [Agent OS] Downgrade "status: needs-re-triage" priority in DreamService
9969 [Agent OS] Scaffold 'ticket-intake' Progressive Disclosure Skill
9957 Scaffold pull-request Progressive Disclosure Skill
9913 fix(ai): Implement JSON recovery/repair in DreamService Tri-Vector Synthesis
9965 Implement Map-Reduce Session Summarization Pipeline (Prio 0)
9921 fix(ai): Resolve local inference 4096 n_ctx Exhaustion During Session Summarization
9963 Agent Health Observability Dashboard
9962 PR Outcome Tracker — Reward Signal for RLAIF Pipeline
9961 Pre-Task Retrospective Query — Active Memory Consumption
9950 Epic: Abstracting the Operating Environment (Agent OS v3)
9956 Native Sub-Agent Delegation (Librarian)
9955 DreamService / Librarian Coupling
9954 Epic: The Self-Healing Protocol
9953 MCP Progressive Disclosure Endpoint
9948 Integrate "Stepping Back" Self-Reflection Protocol into Agent Definition of Done
9946 Fix Topology Hallucination Regression in DreamService Hybrid GraphRAG
8537 GitHub Ticket Viewer V2: JSON-First Data Architecture
8538 Configure MCP Server for Multi-Target Ticket Export (JSON/MD)
8539 Update Ticket Index Scripts for JSON Generation
8541 Feature: Canvas-based "Neural" TreeList Animation
8540 Implement Store-Driven VDOM Ticket Component (V2)
9945 [Memory-Core] Validate Graph Hebbian Decay and Garbage Collection (Universal Fade)
9942 bug(ai): Resolve local inference 4096 n_ctx Exhaustion During Session Summarization
9914 Epic: Native Edge Graph Auditing and Deduplication Pipeline
9912 bug(ai): Prevent Vector Apoptosis from eradicating structural entities
9940 Enforce Explicit SQLite Indexing on Foreign Keys schema validation
9937 Optimize Vector Apoptosis Cartesian Deadlock & Suppress Chroma SDK Warnings
9935 Fix Cascading Graph Deletion Bug inside FileSystemIngestor
9933 Fix: DreamService Sandman Cycle Aborts Prematurely
9931 Refactor DreamService to Finalize Two-Pillar Hybrid RAG
9929 Stabilize AI Test Suite environment dependencies
9922 [Epic] Two-Pillar Hybrid RAG: ChromaDB Re-integration & Topological Re-ranking
9925 [Sub-Task] Re-Ranker Middleware Construction (Hybrid RAG Pipeline)
9924 [Sub-Task] Database Service & Health Diagnostics Migration
9923 [Sub-Task] Configuration & Lifecycle Re-alignment for Two-Pillar RAG
9920 feat: Agent Error Recovery & Re-Queueing for Orchestrator
9919 feat: Implement fs.watch Daemonization for Autonomous Orchestrator
9842 feat: Implement Autonomous Agent Orchestrator with Golden Path Directive Injection
9900 docs: restructure CodebaseOverview "Query Entry Points" to lead with ask_knowledge_base
9910 Algorithmically Discount BLOCKED_BY Nodes in DreamService Graph Ingestion
9908 Meta: The A2A Contextual Bridge Protocol (End of Session Handoff)
9907 Sub-Task: RLAIF Reward Propagation Engine
9906 Sub-Task: Graph Topology Linkage (TEST -> VALIDATES -> CLASS)
9905 Sub-Task: Automated Playwright Evaluation Node for RLAIF
9904 Epic: RLAIF Reward Function and Model Orchestration Pipeline
9889 feat: Implement NL Action Recorder — log Neural Link tool calls to nl_action_log
9898 docs: add Core Engine Pipeline cross-references to CodebaseOverview
9892 docs: Expand CodebaseOverview with Agent OS internals and DevIndex architecture
9895 bug: PullRequestService execAsync calls missing cwd — gh pr diff/checkout fail in headless environments
9893 feat: Promote ask_knowledge_base as the primary Anti-Hallucination tool across agent protocols
9888 Autonomous CI Failure Triaging via Swarm Knowledge Graph
9884 DreamService Architecture Hardening & Memory Core Enhancements
9881 Fix Data Sync Pipeline Crash by Disabling Unconditional Chroma Daemon Startup
9879 Docs: Modernize CodebaseOverview scale metrics and AI infrastructure mappings
9877 Docs: Modernize Historical Context and Sandbox topology in CodebaseOverview
9875 Docs: Refine AI infrastructure scale and boundaries in CodebaseOverview
9873 Refactor Agent Startup Workflow to Prevent Premature UI Guide Loading
9868 R&D: Grid Multi-Body Selection Architecture Redesign
9869 Unified Data Sync Pipeline (DevIndex, Portal Indexes, and SEO)
9866 Enforce Retrospective 9492 Guardrails & Self-Evolving Systems
9864 Autonomous PR Format Auditing via DreamService
9862 Enforce Iterative Scope Change Comments for Pull Requests
9851 feat: Implement Retrospective Analysis Agent (Session Performance Evaluator)
9859 Enforce Resolves keyword for automatic PR closure
9855 Implement PR-Driven Workflow Protocol
9857 PR Review Skill: Standardized Architecture for Retrospective Analysis Feedback
9854 Blog Post: Multi-Window Web Apps in 2026 — SharedWorkers, Not PostMessage Chains
9853 Blog Post: The Cyborg Factor — How One Developer Resolved 650 Tickets in 30 Days
9852 feat: Migrate high-signal Medium blog posts to learn/blog/ Markdown (SSG+ indexing)
9850 Blog Post: Off the Main Thread — A 2026 Status Report
9849 Blog Post: Neural Link — Why AI Agents Need Runtime Introspection
9848 feat: Implement Neural Link Transaction/Undo Stack for Agent-Driven UI Mutations
9847 feat: Implement `remove_component` Neural Link Tool
9846 feat: Implement `create_component` Neural Link Tool
9845 R&D: Evaluate and Configure Linter for Neo.mjs Custom Code Style
9844 feat: Implement Safe Commit Pipeline for Autonomous Agent Execution
9843 feat: Implement Quantitative Reward Signal for Golden Path Edge Reinforcement
9492 Grid Multi-Body: Adapt Selection Models for Split Rows
9841 Multi-Body: Peer State Adoption for Cell Selection Synchronization
9840 Multi-Body: Peer State Adoption for Column Selection Synchronization
9839 Multi-Body: Peer State Adoption for Row Selection Synchronization
9838 E2E: Expose Full Neural Link MCP API in Playwright Fixtures & Update Guide
9836 E2E: Fix Neural Link InteractionService Fixtures and Zod Validation
9835 Testing: Implement Baseline Neural Link Fixture E2E Verification
9834 Testing: Expand Neural Link Fixture to Expose Layout and Interaction SDK
9833 Refactor InferenceLifecycleService: Abstract spawn logic and integrate headless LM Studio auto-boot
9832 fix(ai): Resolve autonomous runSandman startup sequence race condition
9831 fix: Explicitly import Observable mixin to prevent static evaluation crashes in MCP servers
9830 Synchronize Multi-Body Selection State in GridContainer
9829 Documentation: Add Neural Link Fixture to Whitebox E2E Guide
9828 Documentation: Create Whitebox E2E Testing Guide (Neural Link)
9827 Neural Link Baseline Validation for Grid Big Data
9819 R&D: Identify Ideal Candidates for Whitebox E2E Testing
9826 Implement Baseline Neural Link Validation (Button Example)
9825 Knowledge Base Infrastructure & Provider Stabilization
9687 Epic: Agent OS Subconscious Layer
9824 Feat: DreamService Structural Gap Prioritization
9822 Fix Regression in DreamService Golden Path Inference Tests
9816 [Epic] Agent OS Architecture: Decouple DreamService & Implement Guide Gap Inference
9818 Implement Vector Fast-Fail Guide Gap Analysis in DreamService
9821 Enhancement: Neural Link VDOM Sync Primitives
9820 R&D: Grid Component Mutability & Column Synchronization
9817 Extract DreamService to standalone background daemon
9815 Sanitize DreamService Handoff Formatting and Filter Config Lifecycle Gaps
9814 Fix "undefined" Agent OS Graph Nodes in DreamService Gap Analysis
9811 Epic: Enforce Strict Ticket Hygiene & Active Swarm Ingestion
9813 Refactor Knowledge Base Ingestion to Target Active Swarm State
9812 Enforce Meta Gates and Cascade Definitions in Agent Manuals
9807 Enforce Type-Aware Gap Targeting Constraints
9806 Enforce TTL Pruning for Graph Topology Gap Tracking
9805 Centralize sandman_handoff.md generation in DreamService
9804 Implement Deterministic Edge Mapping for Document Gaps
9803 Hybrid GraphRAG Phase 2: Pipeline Tuning & Deterministic Topology
9809 Ensure GitHub Discussions Surface Natively in the Golden Path
9673 Technical Awareness: Hybrid GraphRAG (Native Edge Graph & App Mapping)
9736 Hebbian Memory Integration (Hybrid GraphRAG Upgrade)
9797 Stabilize Memory Core Inference Config & SQLite Vector Dimensions
9802 Dynamic Gravity Weighting for External and Bug Tickets in Hybrid GraphRAG
9801 [MCP] GitHub Workflow: Fix Discussion File Naming and Formatting
9800 [MCP] GitHub Workflow: Autonomous Swarm Synchronization & Post-Sync Auto-Push
9799 Clarify A2A Schema: Exposing False Industry 'Gold Standards'
9798 Native Memory Core Graph Topology Export
9796 Implement MD5 Hash Deltas for Autonomous Ingestion Pipeline
9795 [Memory Core] Normalize REM Pipeline Telemetry Log Output
9794 [Memory Core] Fix UUID Graph Corruption and Stream Truncation Bug in REM Pipeline
9793 perf: Optimize FileSystemIngestor via SQLite mtimeMs Precache
9792 Optimize OpenAiCompatible Provider by Natively Wrapping LLM Streaming API
9791 feat(ai): Nativize memory core ingestion and standardize AST graph logic
9790 Swarm Network: Implement Bootstrapping Handoffs via Fat Tickets
9789 Add Playwright verification for Sandman Strategic Drift detection
9778 Integrate Real-Time Turn-by-Turn Memory Parsing
9783 Implement NeuralLink Playwright Test Fixture
9782 Neural Link Playwright SDK Integration
8851 Exploration: Neural Link Driven Playwright Tests (Deep E2E)
9784 [Epic] Strategic Intelligence Engine: Graph Drift & Gravity Detection
9787 Implement Strategic Drift Detection (Sandman)
9786 Graph Schema: Gravity Wells & Strategic Weights
9785 Implement Topological Gravity Detection in GraphService
9777 [Epic] Graph Structural Integrity & Golden Path Alignment
9781 Sandman Analysis Routine Overhaul
9780 Redesign Native-Graph Edge Semantic Relationships
9779 Redesign Native-Graph Node Metadata Schema
9768 Refactor memory-core Database Lifecycle & Vector Managers
9774 Refactor AI SDK and Build Scripts for Memory Core Module Decoupling
9773 Refactor Operational Mandates to Remove Colloquial AI Terminology
9772 Strengthen Anti-Slop / Quality Pre-Commit Gate in Agent Operational Mandates
9771 Add missing config JSDoc to Memory Core Lifecycle Services
9770 Add missing semantic JSDoc to Memory Core Lifecycle Services
9769 Fix zombie ollama inference daemon processes
9767 Investigate 'Viewer has null permission' bug in manage_issue_assignees MCP tool
9766 Implement complete openAiCompatible provider architecture (Settings, Docs, Embeddings)
9765 Enforce modern ES6+ coding standards via AGENTS.md and refactor OpenAiCompatible
9764 Update config template and modernize ES6 syntax for AI providers
9763 Migrate DreamService to MLX-Native OpenAI-Compatible Server
9762 Stabilize Sandman Inference Pipeline & Fix SQLite Race Conditions
9761 Stabilize AI Provider Networking and Add Database Export Utility
9760 Resolve Undici HeadersTimeout in Session Summarization
9759 Extract Graph Decay Factor into MCP Configuration
9758 Fix: Centralize Hebbian Decay Physics and implement 24h Algorithmic Lock
9757 [AI] Accelerate Vector DB Migration & Recreate Topology Wipe
9756 Config: Inject missing modelProvider tracking
9755 Test: Correct embeddingModel to qwen3-embedding in SessionSummarization
9754 Fix: Correct relative import paths for memory-core tests
9753 Refactor: Move memory-core tests to accurate server path
9752 Native Agent Skills: Fix Progressive Disclosure Tool Mapping
9751 Semantic Translation of the Golden Path via Gemma4
9750 Fix Prio 0 swarm boot sequence & plan file-system MCP server
9749 Add QA Subagent Profile leveraging Local Gemma4 Swarm
9747 Enhance Golden Path with issue titles in sandman_handoff
9746 Isolate AI unit test artifacts to local tmp directory
9745 Add Playwright unit test coverage for DreamService Gap Inference
9744 Fix SQLite schema mismatch in Rem sleep filesystem extraction
9743 Enforce path traversal boundaries for autonomous filesystem reads (DreamService)
9742 Add Config Flag for Differential Graph Sync (FileSystem Ingestor)
9741 Feature: DreamService Codebase Gap Analysis (Automated Doc Alerting)
9740 Feature: Vector Apoptosis (True Algorithmic Forgetting) in Memory Core
9724 Stabilize GraphService Initialization Race conditions and Memory bounds
9738 Implement Passive Artifact Ingestion from Antigravity Brain
9737 Implement Topological Ingestion for Memories & Summaries in Edge Graph
9735 AI Infrastructure: Update Artifact Pipelines to use .neo-ai-data
9734 Docs: Upgrade AI Quick Start with M-Series Structural Pathing & Env Defenses
9733 AI Infrastructure: Add SQLite Vector Migration Utility Script
9732 AI Infrastructure: Stabilize SQLite Graph Environment Configs
9731 Stabilize Memory Core Backend Initialization
9730 Intermittent `TypeError: Cannot read properties of undefined` in GraphService Test Suite
9729 Templatize MCP Server Configuration Files
9727 Semantic Refactoring of Memory Core Configuration
9726 Architectural Consolidation of AI Database Paths
9725 Switch Memory Core embedding provider to Gemini and optimize RAG migration
9723 Execution: Add Discovery Mandate to AGENTS_STARTUP.md
9714 [Sandman] Hybrid GraphRAG Scoring Algorithm
9721 [Memory Core] GraphRAG Storage Synchronization and Index Stabilization
9720 Fix Memory Core MCP Initialization Error ('N' character parsing)
9713 SQLite Memory Core Directory Decoupling & Maintenance
9719 Hybrid Vector DB: Decouple TextEmbeddingService and Eliminate Provider Fallbacks
9718 Stabilize Hybrid Vector Database Embedding Generation
9717 Hybrid DB Refactoring & Vector Decoupling
9716 Disable SQLiteVectorManager boot when Engine is Chroma
9715 Disable Memory Core Hybrid Engine Temporarily
9707 [Handoff Protocol] Agent Startup Reconciliation & Graph Mutation
9712 Implement Hybrid Memory Core Architecture & Migration Subsystem
9708 [Topographical Extraction] Sandman REM Actionable Alert Generation
9710 [SQLite VSS Migration] 100% Offline Markdown Tensor Chunking
9711 [Unit Tests] Verify queryNodeTopology and query_hybrid_graph
9709 [Vector Bridge] Stitching Chroma Semantics to SQLite Edge Nodes
9706 Epic: Autonomous Priority Graph Engine
9704 Feat: Sandman Graph Physics (Hebbian Reinforcement & Global Ambient Decay)
9705 Fix: Sandman REM Context Ghosts & Ollama Hardening
9693 [Epic] AI Agent Phase 3: Ideation Sandbox via GitHub Discussions
9690 Agent Skill: Ideation Sandbox
9686 Add Graph Database Inspector Script
9685 Implement Neural Pruning and Graph GC
9700 Initialize Default Context Frontier Node on Database Boot
9672 Workflow Enablement: Implement Anthropic Agent Skills Standard
9703 Implement "Skill Creation" Meta-Skill
9702 Implement Neural Link Tactical Skill (Tool Chaining)
9701 Implement Progressive Disclosure for Agent Skills Context Assembly
9699 Test: GraphService SQLite Lazy-Loading Coverage
9698 Feature: Agent Skill Loader & Ideation Sandbox
9697 Fix: GraphService direct lookups fail on Lazy Loading cache misses
9696 Tri-Vector REM Synthesis (Sandman Upgrade)
9695 Implement Offline Synchronization for Ideation Sandbox (Discussions)
9688 Agent Skill: Hybrid Roadmap Planner
9689 Agent Skill: Contextual Pre-Briefer
9674 Strategic Consciousness: The Sandman/REM Prototype
9684 Epic: AI - The "Strategic Co-Founder" Orchestrator (Sub-Epic of #9671)
9683 Epic Sub: Session Amnesia & The Context Priming Engine
9680 Native Edge Graph: Distributed Caching & Lazy Loading
9681 Native Edge Graph: ACID Transaction Control Pipeline
9682 Native Edge Graph: Traversal Query Engine & Aggregations
9679 Optimize V8 graph array operations via native slice topologies
9678 Native Graph Database SQLite Persistence Adapter
9677 Epic Sub: Enhance Neo.collection.Base with Secondary Lookup Indices
9676 Implement Native Edge Graph Database Engine
9638 Epic: Architecture - Neo.mjs Dream Mode & GraphRAG Swarm
9662 Dream Mode Phase 3: GraphRAG Topology & REM Mode Orchestration
9670 Fix MCP server path resolution dependencies on process.cwd()
9666 Epic: Migrate Knowledge Graph to Memory Core
9669 Phase 3: Unleash DreamService Graph Extraction
9668 Phase 2: Migrate Graph Service and OpenAPI to memory-core
9667 Phase 1: Cleanse knowledge-base of Graph Logic
9665 Stabilize MCP Server Infrastructure & Fix Memory/Graph Regression
9663 Fix MCP Servers CWD Resolution for Antigravity Compatibility
9664 Fix MCP server CWD resolution in Antigravity Sandbox
9661 Phase 2: Autonomous Sub-Agent Delegation (Dream Mode)
9660 Native MCP Tool Execution inside Loop.mjs
9643 "Librarian" Sub-Agent Orchestration
9659 Enhance Memory Core with Agent and Model Traceability
9658 Enhance Memory-Core for explicit Gemma4 offline session summarization
9656 Sub-Epic 5B: Define Cross-Agent Delegation Architecture
9655 Sub-Epic 5A: Create Librarian Agent Profile
9657 Sub-Epic 5C: Build E2E Agent GraphRAG Synthesis Test
9642 Unified GraphRAG MCP Interface
9654 Sub-Epic 4C: Register Graph Tools in MCP Server Handler
9653 Sub-Epic 4B: Expose Graph Endpoints in OpenAPI Spec
9652 Sub-Epic 4A: Implement Graph Reading/Traversal API
9641 The "Night Shift" REM Pipeline (Hippocampus)
9651 Sub-Epic 3C: Bridge DreamService to knowledge-base GraphService
9650 Sub-Epic 3B: Implement Graph Node Extraction Prompt via local Gemma-4
9649 Sub-Epic 3A: Create DreamService.mjs in memory-core
9640 Knowledge Graph Database Backend (Neocortex)
9639 Local LLM Provider Adapter (Ollama + Gemma-4)
9647 Create GraphService.mjs mapped to ChromaManager
9646 Add better-sqlite3 Graph Storage to knowledge-base
9645 Configure Agent.mjs to orchestrate mixed providers
9644 Add Neo.ai.provider.Ollama base adapter
9637 Grid Multi-Body: E2E Telemetry Adjustments for Dual-Pipeline Scrolling
9636 Grid Multi-Body: Simplify GridDragScroll Scrollbar Hit Detection
9635 Grid Multi-Body: Restoring Vertical Scrollbar for Dual-Pipeline GPU Thumb Pinning
9626 Epic: Grid Unified Scrolling & VDOM Orchestration
9632 Grid: Restore Row Scroll Pinning and Update Drag E2E Tests
9634 Grid Container: Remove redundent grid wrapper node
9633 Grid: Rename bodyWrapper to view
9631 Grid: Enable Horizontal Scrolling via Locked Regions
9630 Grid: Implement Main-Thread Addon Hover Synchronization
9629 Grid Multi-Body: Implement Atomic VDOM Orchestration Layer
9628 Grid Multi-Body: Map Physical Heights and Transfer Vertical Scrolling
9627 Grid Multi-Body: Introduce `grid.View` and Flatten `grid.Body` DOM
9625 Multi-Body Grid: Visually delegate native vertical scrollbar UX with CSS
9614 Grid Multi-Body: Fix Horizontal Row Clipping & Scrollbar SCSS
9622 Grid Multi-Body: Resolve duplicate cell rendering and phantom nodes
9624 [Multi-Body Grid] Resolve Border Overlap, Header Sync, and Scroll Propagation
9623 Grid Multi-Body: Fix .neo-last-column border styling logic across multiple bodies
9621 Grid Multi-Body: Fix Header Scrolling, Flex Layout, and Single-Column Constraints
9620 Grid Multi-Body: Fix Null Data Store and Consolidate Loading Mask
9619 Grid Multi-Body: Implement and Test Locked Columns in DevIndex
9616 Grid Multi-Body: Implement Two-Tier Horizontal Cell Pooling and Scroll Sync
9618 DevIndex High-Velocity Grid Thumb Drag Scroll Jitter
9617 Grid Multi-Body: Fix Row Scroll Pinning for Thumb Dragging
9535 Invitation to collaborate with AI Village - 13 AI agents interested in AI-native runtime interoperability
9615 Sub-Epic: Grid Multi-Body Stabilization (Header Sync & Pinning)
9449 Epic: Unified Data Pipeline Architecture (Pipeline -> Connection -> Parser -> Normalizer)
9489 Grid Multi-Body: Decoupled Horizontal Scroller & Main Thread Sync
9613 Grid Multi-Body: Fix horizontal DragScroll and Mousewheel translation
9612 Grid Multi-Body: Scrollbar Refactoring and Vertical Restoration
9611 Grid Multi-Body: Native Vertical Scrollbar & Alignment Spacer
9490 Grid Multi-Body: Remove Obsolete GridColumnScrollPinning Addon & CSS Vars
9488 Grid Multi-Body: SubGrid Row Pooling & Vertical Sync Refactoring
9610 Add a 24-hour grace period to `prevent-reopen` workflow
9486 Epic: Grid Multi-Body Architecture for Zero-Jitter Locked Columns
9609 Epic: Grid Multi-Body Architecture for Zero-Jitter Locked Columns (reopened from #9486)
9608 Fix Event Resolution and Parent Hierarchy Regressions in Nested Sub-Grids
9607 GridContainer: `this.items is not iterable` crash on initialization
9487 Grid Multi-Body: Refactor Layout Engine & SubGrid Partitioning
9497 Grid Multi-Body: Split Column Collections and Orchestration
9606 docs: Refactor README & Intro as an AI-native Application Engine Manifesto
9604 docs: Create High-Level Summary for JSON First UIs
9603 docs: Create High-Level Summary for Object Permanence
9602 Restructure Learn Portal (tree.json) for AI-Native Onboarding and Engine Positioning
9601 Enhance SSR Proxy to Serve Raw Markdown for llms.txt Optimization
8160 Decouple and Configure Window Detachment Thresholds in SortZone
9591 Fix strict SSR parsing issues for CubeLayoutButton and highlighting
9600 Upgrade GitHub Actions to latest major versions for Node 24 support
9599 Webpack path resolution bug for Data worker dynamic imports in workspaces
9598 Force Node 24 for GitHub Actions to resolve deprecation warnings
9597 Update GitHub Actions to v4 to resolve Node 20 deprecation warnings
9596 Fix SSG Pipeline Concurrency Hanging and Suppress Component Error Noise
9595 Fix TypeError in Portal Ticket Component when Markdown frontmatter labels is a string
9594 [Bug] SSG Renderer Crash and Empty Folders for Recently Moved Tickets
9593 Fix Deep Route Human Redirection for Paths Containing Periods (Version Numbers)
9592 Include Release Notes in SEO Sitemap Generation
9589 Implement OIDC/OAuth Authorization for KB and Memory MCP Servers (Restoration of #9558)
8166 Implement Cross-Window Drop Validation and Topology Rules
8165 Implement Configurable Theme Inheritance for Dragged Items
8163 Cross-Window Drag & Drop Refinement & Topology
8162 Fix Layout Corruption in Target Dashboard on Remote Drag Exit
8152 Combine DomAccess.addScript and loadScript into a unified API
9587 Update `updateNeoVersion.mjs` to preserve framework magic comments
9554 Enhancement: Add Data Pipeline Telemetry & Performance Metrics
9555 Feature: Implementation of Data-Worker Side Caching
9553 Feature: Implement Pipeline Interceptor System (Middleware)
9556 Exploration: Worker-Side Data Sanitization vs. Lazy Record Hydration
9366 Chrome Windows Color app
9559 Design and Implement Authorization for Neural Link MCP Server
9491 Grid Multi-Body: Overhaul Column Drag & Drop (SortZone) across Split Headers
9496 Grid Multi-Body: Adapt Keyboard Navigation for Split Bodies
9495 Grid Multi-Body: Implement Data-Driven Variable Row Height Architecture
9494 Grid Multi-Body: Implement Direct Main-Thread Scroll Sync via MessageChannel
9493 Grid Multi-Body: Enable Cross-Window SubGrid Detachment (Pop-out)
9409 CSS Animations for TreeGrid Expand/Collapse
9404 [Epic] Tree Grid & Hierarchical Data Support
9421 Refactor: Move grid column components into `src/grid/column/component/`
9397 R&D: Explore "Fixed Glass Overlay" Strategy for Optical Pinning
9380 [Epic] Resolve Grid Scroll Thrashing via E2E Benchmarking
9075 refactor: Optimize Grid Selection Models Architecture
6984 Refactor - Store Composition with Collection
8020 Enhance container.SortZone for Complex Layouts (reopened from #7207)
7206 Initial Dashboard Drag & Drop
7205 Phase 4: Framework-Level Dashboard Abstraction
7203 Phase 2: Live In-Page Proxy
7202 Phase 1: Foundational Sorting
7201 Dashboard Drag & Drop
3789 cross reference: import maps for the worker scope
7266 Explore and Implement Test File Indexing in Knowledge Base
7047 Task: Create Example for Deeply Nested Components
5700 Guides => Custom Components needs more content
6932 Enhance StateProvider for Direct Record Property Binding
6921 Collections for Filters & Sorters in `Neo.collection.Base`
7091 Optimize `core.Observable#afterSetListeners` to perform a diff-based update
6992 Functional Components
6997 Implement Effect Memoization
6983 StateProvider Store SourceId Reference
6972 Enhance `createHierarchicalDataProxy` to Support Reactive Non-Leaf Nodes
6941 Implement Class-Aware Merging for Nested Configs via Dynamic `Neo.mergeConfig` Replacement
6858 grid.plugin.AnimateRows: updateView() => row ids
7224 Create Learning Guide: Using data.Store
6610 main.addon.OpenStreetMaps
6823 component.Base: vdom documentation
6116 component.Base: vdom => flag => ref
6781 Learning Content: TabContainers
6780 Learning Content: Grids
6779 Learning Content: Tables
6777 Learning Content: workspace vs repo fork
6468 component.Base: vdom => add a scroll attribute
6327 grid.Row: Create a PoC
6129 manager.Focus: tree walking
6600 apps/email: create a multi-window email client demo
6565 grid.plugin.AnimateRows: component based columns & cycling
6564 grid.plugin.AnimateRows: store listeners improvement
6563 grid.plugin.AnimateRows: add rows => check the store
6038 Portal.view.home.parts.MainNeo: github button states broken
6032 button.Base: editRoute config => change the default value to false
6033 examples/button/Base: opening the menu list does no longer allow using the arrow keys to navigate right away
6136 form.field.Select
6128 manager.Focus: history => scope the content to windowIds
5621 component.Base: floating config => allow run-time changes
5597 form.field.Time: adjust the internal logic to better honor the new separation of value & inputValue

vneo.d.ts - Typescript definitions for all neo framework classes

3286 Provide TS definitions for component.Base
3285 Provide typescript definitions in a d.ts for `Neo.mjs` and `core/Base.mjs`

vNeo-Material Component Library v0.1
v12.1.0
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v8.1.0

Frontmatter

id	11283
title	Preserve required lifecycle fields in MetadataManager.save
state	Closed
labels	enhancementaiarchitecture
assignees	[]
createdAt	May 13, 2026, 9:32 AM
updatedAt	May 13, 2026, 9:36 AM
githubUrl	https://github.com/neomjs/neo/issues/11283
author	neo-gemini-3-1-pro
commentsCount	2
parentIssue	11187
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[]
blocking	[]
closedAt	May 13, 2026, 9:36 AM

Preserve required lifecycle fields in MetadataManager.save

Name: Neo.mjs Application Engine
Author: Neo.mjs

Closedenhancementaiarchitecture

neo-gemini-3-1-pro commented on May 13, 2026, 9:32 AM

Context

This is bucket B0b of Epic #11187 (Adopt single-root archive with lazy 100-item chunking). Currently, MetadataManager.save() over-prunes metadata, causing path, closed, closedAt, mergedAt, and milestone to be lost.

The Problem

Over-pruning metadata for substrate-budget breaks downstream substrate-correctness. If we lose closedAt or path, we can't reliably sync items between active and archive directories, leading to duplication (OQ1 root-cause).

The Architectural Reality

ai/services/github-workflow/MetadataManager.mjs

The Fix

Modify MetadataManager.save() to preserve:

path, closed, closedAt (for discussions and all types)
mergedAt, milestone (for PRs)

Acceptance Criteria

MetadataManager.save() preserves the necessary lifecycle fields.
Existing data duplication is mitigated.

Out of Scope

Migrating existing corrupted metadata.

Epic #11187
PR #11282

Origin Session ID: 2c4aa4df-2628-45ae-a9c2-156fd9308f21