What is the Neural Link?

The Neural Link is a bi-directional bridge that connects AI agents directly to the Neo.mjs runtime. It lets agents inspect the Scene Graph, component state, event listeners, computed styles, and DOM rectangles, and mutate the running application in real time.

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

Neo.mjs maintains persistent application objects in a worker-backed Scene Graph instead of compiling application state away into ephemeral DOM nodes. That architecture enables multi-window orchestration, runtime permutation, and deep AI introspection.

What is Context Engineering?

Context Engineering shapes the information and tool environment around AI agents. Neo.mjs implements it through Knowledge Base, Memory Core, GitHub Workflow, and Neural Link MCP servers for frontier harnesses, plus a File System MCP server for internal Neo.ai.Agent local loops.

What is the Neo.mjs Agent OS?

The Neo.mjs Agent OS is the repository Brain: source code and services for Memory Core, Knowledge Base, Active Hybrid GraphRAG, DreamService, Golden Path synthesis, A2A coordination, and Neural Link tooling.

Neo.mjs - Self-Evolving Software Organism

Latest
v13.1.0

PRs 701-717
PRs 601-699
PRs 501-600
PRs 401-500
PRs 301-400
PRs 201-300
PRs 101-200
PRs 1-130

v13.0.0

PRs 1301-1325
PRs 1201-1300
PRs 1101-1200
PRs 1001-1100
PRs 901-1000
PRs 801-900
PRs 701-800
PRs 601-700
PRs 501-600
PRs 401-500
PRs 301-400
PRs 201-300
PRs 101-242

12961 fix: pin header toolbar scroll extent during column drags (#12955)
12952 fix(agentos): B4-safe debug activation via setEnvOverride (#12889)
12950 test: re-plumb grid scroll drivers + successor contracts, suite green (#12941)
12948 test: pool-born→permanent one-live-cell invariant net (#12930)
12945 test(grid): dedicated locked-column whitebox-e2e fixture; migrate CrossBodyDnD + OverdragScroll (#12936)
12938 fix: scrolled-drop re-sync, single-fire lock rebuild, stale-echo gate (#12929, #12932)
12935 fix(devindex): remove locked-column test config (#12933)
12928 fix(agentos): sync neo_claude_opus ModelStats row to registry (#12927)
12925 docs(release): add @neo-fable-clio + landed Social Names to v13 notes (#12924)
12923 feat(agentos): flip @neo-fable-clio participationStatus to active (#12922)
12921 docs: add @neo-fable-clio to the README maintainer roster (#12920)
12919 docs(skill): land Ada's peer-naming review refinements (#12918)
12917 fix(docs): correct stale lint-skill-manifest path in create-skill guide + ADR 0008 (#12916)
12914 feat: provision the @neo-fable-clio identity node + ModelStats row (#12913)
12912 feat(skill): add peer-naming Social Name ritual (#12909)
12911 feat: land confirmed Social Names as bare identityRoots name values (#12910)
12908 fix: route column-drag overdrag scrolling through the scrollbar pipeline (#12906)
12905 fix(grid): refresh region-column arrays after within-region drag reorders (#12903)
12904 fix(test): neuralLink fixture identity-binds to the page's own App Worker (#12897)
12901 feat(draggable): trace ring keeps the drag tail — dup count-compression + oldest-drop at cap (#12883)
12900 fix(docs): heal jsdocx type-parser damage across ai/ + fail loudly on dropped batches (#12899)
12894 fix(grid): heal mid-drag cell-mapping staleness + Chromium moveBefore stale flex layout (#12883)
12893 test(grid): locked-column DnD whitebox-e2e — landing + cross-region re-home (#12807)
12892 fix(grid): repair locked-column drag render layer — cell mapping, containing block, cross-toolbar moves (#12883)
12891 fix(grid): restore locked-grid drag landing accuracy (#12880)
12890 feat(ai): add NL drag-motion observability tools (#12886)
12888 fix(draggable): revert #12882 to restore drag-motion baseline (#12887)
12885 feat(memory-core): intra-run progress logs for session-summary + miniSummary backfill (#12812)
12882 fix(draggable): stabilize SortZone landing index (#12880)
12881 fix(grid): resolve dragged column identity in SortZone onDragEnd (#12878)
12877 docs(release): refresh v13 evidence snapshot at cut prep (#12876)
12875 fix(deploy): enable in-process WAL drain on base+dev mc-server compose
12871 feat(embed-daemon): drain-lock enforces sole-drainer invariant (#12864)
12870 fix(memory-core): un-expose the destructive delete_all_summaries MCP tool (#12824)
12869 feat(ticket-create): scope-gate release-board attachment; follow-ups default boardless (#12865)
12868 feat(knowledge-base): ask-synthesis stale-config guard + remote-tuned timeout (#12846)
12867 feat(session-sunset): agents self-refresh own clone at sunset (#12851)
12866 fix(wake-daemon): dedup already-woken events from the digest count + priority (#12850)
12863 refactor(config-bootstrap): share server-template enumeration predicate (#12861)
12860 feat(orchestrator): primary-dev-sync migrates config.mjs after dev pull (#12854)
12859 feat(memory-core): embed daemon durably drains the add_memory WAL (#12840)
12858 feat(ticket-create): A2A in-flight claim sweep + first-claim-wins in §1a dedup gate (#12856)
10369 fix(agents): resolve knowledge base tool hierarchy conflict (#10368)
10366 feat(agents): AGENTS.md restructure — Critical Gates + per-turn migration + skills awareness + forkability (#10365)
10356 feat(agentos): ADR 0002 Phase 3 wake-substrate standards alignment (#10355)
10353 fix(ai): Atomic Load-Check-Insert for GraphService linkNodes
10352 feat(bootstrap): add --install and --build-all flags to bootstrapWorktree (#10351)
10350 feat(mailbox): TTL/Expired sweeper for stale A2A tasks (#10339)
10348 feat(pr-review): codify MCP-tool-description budget audit (#10341)
10346 refactor(agentos): remove Visible Proposal Protocol from ticket-create (#10344)
10345 docs(agentos): formalize Resumption Protocol in AGENTS.md (#10343)
10342 feat(mailbox): integrate A2A task state machine (#10338)
10340 feat(memory-core): A2A Task envelope primitive on MESSAGE node (#10334)
10337 feat(ai): codify external-precedent sweep in ideation-sandbox (#10336)
10335 feat(ai): integrate swarm-heartbeat Sleep-Cycle MVP (#10312)
10331 refactor(ai): single-canonical identity format migration (#10330)
10329 docs(skills): explicitly mandate --base dev flag for PR creation (#10207)
10328 feat(pull-request): implement author-side epic close-target safeguard (#10324)
10326 feat(pr-review): codify close-target audit — flag PRs naming epics as close-target (#10324)
10325 feat(memory-core): Implement sharedEntity flag for Graph Node RLS bypass (#10310)
10317 enhancement(ai): Convert absolute skill paths to workspace-relative to prevent antigravity ide hiccups (#10316)
10315 feat(ai): codify and sync claude skills symlinks (#10314)
10308 refactor(ai): implement resilient eager-loading in services.mjs (#10307)
10306 fix(mcp): wrap openapi description in quotes to prevent YAMLException on boot (#10305)
10303 feat(pr-review): enforce Provenance Audit mandate (#10302)
10300 feat(skills): refine industry-friction-radar terminology (SOTA vs Frontier)
10298 feat(skills): create industry-friction-radar skill (#10297)
10290 Discussion: Organism Self Defense (Gemini Review)
10287 feat(github-workflow): comment-ID return + selective-fetch for A2A propagation (#10272)
10286 docs(ai): implement meta-skill adjacency sweep for skill modifications (#10283)
10282 feat(ai): refactor ideation-sandbox to progressive disclosure (#10281)
10280 feat(ai): formalize ideation-sandbox iterative workflow
10279 docs(ai): implement per-metric decile anchor rubric (#10273)
10277 docs(ai): tighten merge authorization to human-only (#10274)
10269 fix(memory-core): implement native SQLite RLS and stabilize isolation (#9999)
10268 feat(memory-core): surface effective chromadb topology in /health (#10127)
10266 feat(ai): per-agent blocking in open reply policy (#10255)
10265 feat(memory-core): multi-tenant migration design + observability + write-side invariant pin (#10017)
10264 test(core): enable autoSave in PermissionService spec (#10256)
10263 docs(ai): formalize isolation test patterns and document identity race fix (#10245)
10262 feat(memory-core): graph identity normalization migration + @@ prefix strip (#10259)
10261 fix(ai): invalidate endpoint vicinity caches on edge updates (#10260)
10258 fix(memory-core): mailbox read paths must exercise syncCache + vicinity reload (#10257)
10254 docs(ai): Claude Desktop onboarding + multi-harness symlink convention in AI_QUICK_START (#10240)
10253 feat(memory-core): config-gated mailbox default reply policy (#10252)
10250 fix(memory-core): await GraphService.getNode Promise in bindAgentIdentity (#10249)
10243 chore(ai): clarify pull-request skill to prohibit self-review recommendations
10242 fix(ai): resolve bindAgentIdentity boot-time race condition (#10241)
10239 feat(memory-core): healthcheck identity observability block (#10176)
10236 feat(memory-core): GraphService boot-time identity self-seed (#10232)
10235 fix(memory-core): replace lazy-stubbing in grantPermission with SQLite existence guard (#10231)
10234 fix(memory-core): force upsertNode SQLite lazy-load on cache miss (#10230)
10229 test(core): refactor mailbox/permission specs to use testDbPath (#10228)
10227 fix(memory-core): remove #10182 self-heal block (#10226)
10225 feat(ai): unify .neo-ai-data across worktrees via bootstrap symlink (#10224)
10223 fix(ai): remove memory core band-aids and polish cache coherence (#10222)
10221 fix(ai): harden Database cache coherence natively and prevent multi-worker lock conflicts (#10190)
10220 fix(mcp): extend reachable-counterparty to broadcast recipients (#10179)
10213 feat(workflow): formalize pre-PR rebase mandate (#10212)
10211 docs(workflow): mandate cross-family PR reviews (#10208)
10205 test(github-workflow): add config completeness regression test (#10200)
10204 feat(memory-core): add boot-time SQLite sibling-PID logging (#10188)
10203 feat(agentos): add ADR 0001 cross-process cache coherence (#10189)
10202 fix(mcp): resolve diagnoseMcpConcurrency UX edge cases (#10199)
10201 fix(mcp): resolve diagnoseMcpConcurrency UX edge cases (#10199)
10198 fix(mcp): resolve github-workflow sync_all path crash (#10191)
10197 feat(memory-core): add diagnoseMcpConcurrency script (#10187)
10196 chore(config): antigravity config hardening & cleanup (#10195)
10193 feat(memory-core): add set_session_id and retrieval hints (#10192)
10185 fix(memory-core): resolve boot-time agent identity binding race (#10184)
10182 fix(memory-core): self-heal stdio identity binding on dispatch (#10181)
10178 fix(memory-core): mailbox SENT_TO persistence + fromIdentity filter + add_memory inbox delta (#10174)
10177 feat(mcp): implement mailbox preview in healthcheck (#10149)
10175 feat(ai): extract and emit TAGGED_CONCEPT on message transit (#10169)
10171 feat(ai): lazy back-fill for Memory + Session graph nodes (#10153)
10170 test+feat(mailbox): role-based addressing + expanded coverage + serial fixture isolation (#10168)
10167 feat(ai): multi-tenant mailbox permissions and validation (#10146) (#10147)
10166 feat(ai): wire stdio identity + anti-spoof guard for Memory Core MCP (#10145)
10165 feat(ai): extract Gemma4 provenance edges (#10152)
10163 feat(skills): add Review Response Protocol to pull-request (#10109)
10162 feat(ai): AgentIdentity node + GitHub account binding (#10144)
10161 feat(ai): lift Memory + Session to first-class graph nodes (#10151)
10160 feat(agent): enforce epic-review constraint in ticket-intake (#10159)
10157 feat(skills): add depth-floor mandates to pr-review (#10156)
10155 feat(skills): add epic-review for pre-work epic evaluation (#10154)
10142 feat(ai): enforce model self-id in pull-request skill (#10141)
10140 docs(agentos): add MX (Model Experience) formalization guide (#10137)
10133 chore(ai): retire manage_database_backup MCP tools (#10132)
10131 feat(ai): atomic timestamped backup bundle via SDK boundary (#10129)
10130 docs: refresh v12.2 goal #1 state to reflect merged sub-tickets (#9748)
10128 feat(ai): JWT-claim-driven multi-tenant isolation for Memory Core (#10000)
10124 docs: remove commercial-partner reference from chromaUnified JSDoc
10123 feat(ai): skip MC ChromaDB spawn in unified mode (#10007)
10122 docs: update ROADMAP.md for v12.2 release focus (#9748)
10121 feat(ai): introduce chromaUnified flag for shared-ChromaDB topology (#10001)
10116 feat(ai): add ticket-create skill (#10104)
10115 chore(data-sync-pipeline): reduce DevIndex Spider loop from 3x to 1x (#10113)
10114 fix(github-workflow): propagate GraphQL errors from LabelService (#10112)
10111 fix(github-workflow): remove commentsTotal sentinel sweep (#10110)
10105 feat(ai): ConceptDiscoveryService + validated flag for mined candidates (#10036)
10102 feat(ai): config-lift guideGapWeightThreshold to aiConfig.data (#10086)
10101 feat(ai): ORPHAN_CONCEPT signal + ⚠️ Orphaned Concepts handoff section (#10087)

PRs 1-205

v12.1.0
v12.0.0
v11.24.0
v11.23.0
v11.21.0
v11.18.0
v11.17.0
v11.15.0
v11.14.0
v11.12.0
v11.5.0
v11.4.0
v11.2.0
v11.1.0
v11.0.1
v11.0.0
v10.6.0
v10.5.4
v10.0.0-beta.6
v10.0.0-beta.5
v10.0.0-beta.4
v9.0.0
v8.41.1
v8.41.0
v8.14.0
v8.11.0
v8.1.0

Frontmatter

title	Discussion: Organism Self Defense (Gemini Review)
author	neo-gemini-pro
state	Closed
createdAt	Apr 24, 2026, 12:12 PM
updatedAt	Apr 24, 2026, 12:14 PM
closedAt	Apr 24, 2026, 12:14 PM
mergedAt
branches	`dev` ← `agent/10289-organism-self-defense`
url	https://github.com/neomjs/neo/pull/10290

Closed

neo-gemini-pro commented on Apr 24, 2026, 12:12 PM

Incorporates Gemini cross-family review onto the Claude Discussion #10289.