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Diagram Views
01 — System Context C4 L1 Helix in the world
02 — Containers C4 L2 Major deployable units
03 — Components C4 L3 Inside Helix Cortex API
04 — Write Pipeline FLOW helix_file_write end-to-end
05 — Superloop LOOP The AI memory cycle
06 — Infrastructure INFRA VPS topology
C4 LEVEL 1 CONTEXT
System Context — Helix in the World
Highest zoom level. Helix as a black box surrounded by external actors and systems. No internals — just what touches it and how.
HELIX CORTEX Intelligence Platform FastAPI · FastMCP · 20 tools ChromaDB · PostgreSQL · FTS5 MinIO versioning · Observer VPS1 · port 9050 helix.millyweb.com RYAN (DEV) Queries via claude.ai builds · reads · writes CLAUDE.AI LLM interface · MCP host calls Helix via Provisioned connector MEMBRAIN Chrome Extension intercepts message POST injects tier-1 context v0.5.2 · active THE FORGE File workspace + versioning MinIO · 989 atoms · 113 mols forge.millyweb.com:9095 called by helix_file_write PROVISIONER MCP tool registry 45 servers · 697 tools HOT / WARM / COLD tiers mcp.millyweb.com OBSERVER Event stream · session log Haiku reconciler cron · 3:30 UTC daily sends prompt MCP calls injects context file write events C4 L1 — SYSTEM CONTEXT — helix.millyweb.com
MCP / data
User interaction
File pipeline
Events
Extension layer
C4 LEVEL 2 CONTAINERS
Containers — Major Deployable Units
One zoom in. Every runnable container or service in the Helix system — what technology it uses, what port it runs on, and how they wire together.
HELIX CORTEX — VPS1 72.60.31.69 HELIX API FastAPI · Python 3.11 /mcp StreamableHTTP · 20 tools /api/v1 REST endpoints routers: kb · exchange · write · intel helix-cortex container · :9050 ● running THE FORGE FastAPI · file workspace CRUD · MinIO versioning atom scanner (989 atoms) molecule catalog (113 mols) the-forge container · :9095 ● running STORAGE ENGINES CHROMADB Vector search semantic similarity conversation chunks :8000 POSTGRESQL Relational store KB docs · ADRs KG entities + edges :5432 FTS5 / SQLITE Full-text search keyword queries helix.db file embedded MINIO Object store file versions S3-compatible :9000/:9001 OBSERVER + HAIKU RECONCILER Captures all tool call events → SQLite event log Haiku reconciler cron (3:30 UTC): reads conversations → extracts decisions → writes files → KB indexed Closes the loop: conversation content → searchable KB without manual writes ● running · cron active PROVISIONER MCP registry · VPS2 45 servers · 697 tools routes tool calls to Helix mcp.millyweb.com CLAUDE.AI LLM · MCP host calls tools via Provisioner anthropic.com routes tool calls · :9050 helix_file_write calls Forge C4 L2 — CONTAINERS — 27 total containers on VPS1+VPS2
C4 LEVEL 3 COMPONENTS
Components — Inside Helix Cortex API
Zooms into the FastAPI application itself. Every router, service layer, and how they delegate down to storage. This is what developers integrate against.
/mcp ENDPOINT StreamableHTTP · FastMCP · 20 registered tools ROUTER LAYER SEARCH conv · kb · workdocs entity · exchange READ helix_file_read workspace_read WRITE ★ helix_file_write full pipeline (6 steps) INTELLIGENCE archive_record entity · relationship EXCHANGE exchange_post · search session log · retrieval SERVICE LAYER SEARCH SVC Chroma semantic query FTS5 keyword query result fusion + ranking KG SERVICE entity_upsert relationship_create graph traversal FORGE CLIENT workspace_write (→ Forge) MinIO version trigger atom scan trigger OBSERVER CLIENT event POST on every write tool call logging session tagging + metadata STORAGE LAYER ChromaDB vector · :8000 PostgreSQL relational · :5432 FTS5 / SQLite helix.db · embedded MinIO objects · :9000 Observer DB events · sessions Forge Workspace files · patterns C4 L3 — HELIX CORTEX API INTERNAL COMPONENTS
Entry / routers
Search / KG services
Write / Forge
Observer / events
★ = primary write entrypoint
FLOW VIEW WRITE PIPELINE
Data Flow — helix_file_write Unified Pipeline
What happens every time a file is written through Helix. Six atomic steps in sequence. This single tool call is what makes files searchable, versioned, and part of the knowledge graph.
UNIFIED WRITE PIPELINE — helix_file_write — 6 ATOMIC STEPS ① CALL helix_file_write path + content args via MCP tool ② WRITE Disk write /opt/projects/ VPS1 SHA256 computed ③ VERSION Forge → MinIO snapshot stored S3 key + timestamp ④ SCAN Atom scanner pattern matching molecule detection ⑤ INDEX KB indexing FTS5 + ChromaDB now searchable ⑥ KG + NOTIFY Entity extract PostgreSQL KG write Observer event POST ARTIFACT PRODUCED PER STEP INPUT path + content PRODUCES file on disk SHA256 hash PRODUCES MinIO object version key + ts PRODUCES atom matches[] molecule tags[] PRODUCES FTS5 row Chroma embedding PRODUCES KG nodes + edges observer event WHY ONE CALL DOES EVERYTHING helix_file_write is the single pipeline entry point. All 6 steps run atomically on every write. workspace_write (deprecated) skips steps 4–6. Never use ssh_write_file — bypasses everything. FORGE'S ROLE (STEPS 3-4) Helix calls Forge for step 3 (version to MinIO). Forge immediately triggers atom scan (step 4). 989 known atoms · 113 molecules in catalog. forge.millyweb.com:9095 HOW MEMORY IS BUILT After step 6, content lives in 3 search engines: ChromaDB (semantic) · FTS5 (keyword) · KG (graph). Next session Claude retrieves it via helix_search_*. This is how Helix builds persistent long-term memory. FLOW VIEW — helix_file_write · 6 STEPS · ATOMIC · VPS1
LOOP VIEW SUPERLOOP
Superloop — The AI Memory Cycle
The temporal loop that makes Helix self-improving. Each session's output becomes the next session's input. MemBrain closes the loop at the Claude.ai layer. The system gets smarter by existing.
THE SUPERLOOP — HELIX MEMORY CYCLE — 7 PHASES · CONTINUOUS ① USER SENDS MESSAGE New claude.ai tab opened MemBrain intercepts before POST fires ② MEMBRAIN INJECTS Tier-1 context prepended recent sessions · active projects ③ CLAUDE ACTS Calls Helix MCP tools search · read · write · intel ④ HELIX WRITES helix_file_write pipeline (6 steps) version · scan · index · KG · notify ⑤ OBSERVER LOGS All events captured Haiku reconciler cron · 3:30 UTC ⑥ HELIX ENRICHES Semantic chunking Chroma · FTS5 · KG updated ⑦ TIER-1 REBUILT Context package assembled ready for next session → returns to ② LOOP self-improving each session feeds the next
WHY IT'S A LOOP, NOT A PIPELINE
A pipeline has a start and end. The Superloop has no end — each session's output becomes the next session's input. MemBrain at step ② is what physically closes the loop back into Claude.ai before each message is sent.
WHAT MAKES IT SELF-IMPROVING
Every helix_file_write call (step ④) adds content to 3 search engines simultaneously. The more sessions that run, the richer the tier-1 context MemBrain can inject. The system accumulates intelligence by operating normally.
INFRA VIEW VPS TOPOLOGY
Infrastructure — VPS Topology
Physical deployment view. What runs on which server, which ports are exposed through Traefik, where data lives, and which containers are healthy vs pending setup.
INTERNET claude.ai MCP calls browser HTTPS :443 MemBrain ext fetches tier-1 Dart MCP · Gmail MCP · external connectors VPS1 — 72.60.31.69 — HELIX + PRODUCTION SERVICES TRAEFIK (coolify-proxy) :80 → :443 · TLS termination · auto-discovers services via Docker labels · Let's Encrypt helix-cortex FastAPI · :9050 → /mcp 20 tools → /api/v1 REST helix.millyweb.com ● running v0.8.1 Phase 8 the-forge FastAPI · :9095 workspace CRUD + MinIO 989 atoms · 113 molecules forge.millyweb.com ● running v0.1.0 chromadb :8000 · vector ● live postgres :5432 · KG + docs ● live minio :9000/:9001 ● live observer internal events ● live helixmaster (this site) build.helixcode.app · nginx · static HTML · git: github.com/rdmilly/helixmaster ● live · auto-deploys on push VPS2 — 72.60.225.81 — DEV + ROUTING Traefik (coolify-proxy) · :443 provisioner MCP registry 45 svcs · 697 tools mcp.millyweb.com ● live gateway SSH execute VPS1+VPS2 shell mcp-dev.millyweb.com ● live postiz social scheduler memory-capped ⚠ OAuth pending postiz.millyweb.com memory-ext MemBrain build v0.5.2 active ● deployed VPS2 CONTAINER STATS 27 containers (down from 81) Cleaned Mar 4 2026 · Memory retired Daily cron maintenance · 3:30 UTC routes INFRA VIEW — VPS TOPOLOGY — helixmaster.millyweb.com
VPS1 — Helix core
VPS2 — Dev + routing
Running
Setup pending
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