Prime-Silo MCP server

Prime-Silo // Sovereign AI Agent OS & Harness

The canonical Sovereign AI Agent OS and runtime harness — engineered for institutional cognition by Binary 16 Labs & Agent Benny.

Explore Live Web Substrate • Read Architecture Spine • View Token Economics

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"Stop gambling with probabilistic cloud wrappers. Start executing with deterministic institutional reasoning."

Prime-Silo is an open-source typed execution substrate and Agent OS harness designed for organizations requiring data sovereignty, zero token tax, and verifiable lineage. It fuses two breakthrough architectures:

• Benny — the deterministic substrate (Pypes Layer 0 transformation algebra, swarm-executed cognitive operations, triple-lineage governance, manifest signing). Vendored here under runtime/.
• Space-Agent — the adaptive shell (browser-resident agent runtime, modular puzzle-piece UI, Git-backed workspace versioning).

🏛️ Why Prime-Silo is Trending in 2026

While traditional agent frameworks suffer from context bloat, cloud gatekeeper fees, and brittle custom code, Prime-Silo delivers:

1. Model Context Protocol (MCP) Native: Universal tool connectivity ("USB-C for AI") without code fragmentation or custom wrappers.
2. Agent-to-Agent (A2A) Swarm Collaboration: Built-in open communication standards for specialized agent swarms to discover and execute tasks autonomously.
3. Zero Token Tax Execution: Deterministic Pypes transformation algebra runs locally, eliminating recursive cloud context dumps and saving up to 90% in token overhead.
4. HMAC SHA-256 Auditable Lineage: Every state transition, UI layout, and decision trace is cryptographically signed and auditable.

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The goal: a single Agent OS shell that gives institutional operators one nav, one theme, one run timeline, and one audit story across documents, code, tabular data, and post-run review — without ever compromising determinism or burning capital on cloud context bloat.

Determinism boundary (ADR-001)

Prime-Silo splits surfaces into two zones, with different agent authority in each:

Zone	Surfaces	Agent authority	Where it lives
Deterministic	Manifest authoring, run execution, KG/code graph mutation, L3 writes, skill registry	Read-only. Drafts → HITL → sign_manifest() → run	Static React widgets
Review (fluid)	Post-run drill-down, frame inspection, reasoning trace, audit query, agent-composed analyst reports	Read everything; write only to agent_sandbox/{views,notes,drafts,skills}/	Adaptive composed canvas

Pinned agent-composed layouts become .aamp.view bundles, HMAC-signed via the existing skin-pack signing path. Replaying a layout is deterministic and auditable.

See runtime/architecture/ADR-001-prime-silo-shell-fork.md for the full decision record, architecture/ROADMAP.md for the rolling phase status, and architecture/OPERATING_PLAN.md for the test runbook + dev loop.

Documentation by Role

👤 Desktop App Users — Start here:

• QUICKSTART-EXE.md — Download, install, and launch the desktop app
• HOME-DIRECTORY.md — Configure where your data is stored
• GUIDE.md — Feature walkthroughs and UI help

💻 Command-Line Users — Start here:

• CLI.md — Complete reference for node space and benny commands
• QUICKSTART-EXE.md — Desktop setup (if needed)
• GUIDE.md — Step-by-step usage examples

🤖 AI Agents — Start here:

• AGENT-AWARENESS.md — System state, API endpoints, sandbox permissions
• CLI.md — Available CLI tools for agents
• HOME-DIRECTORY.md — Workspace file structure

🔧 Developers — Start here:

• AGENTS.md — Architecture rules and contracts
• runtime/architecture/ADR-001-prime-silo-shell-fork.md — Design decisions
• architecture/OPERATING_MANUAL.md — Deep-dive dev setup

📚 Full Documentation Index:

• See INDEX.md for the complete navigation map

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Interactive demo site: site/ — self-contained website that tours every feature (with layer-by-layer deconstruction views), embeds the operating manual, and ships a configuration wizard (generates your .env + prime-silo.config.json + launch commands, each setting mapped to the process that consumes it) plus a live operator dashboard that health-checks your running stack. No build step:

.\scripts\site.ps1            # or: python -m http.server 4173 --directory site
# → open http://localhost:4173

Companion — Memo-Ray: the memory graph of the cognitive mesh — the third first-class graph beside the knowledge graph (documents) and code graph (AST). It X-rays Claude + Antigravity session logs into an explorable organic lineage map so the operator never has to be the institutional memory. Clone it beside this repo (or set MEMORAY_DIR); .\scripts\dev.ps1 auto-boots it when enabled.

As of Phase M1 the memory graph is built into the shell — one capability on four surfaces, all over a single configurable proxy (/api/memoray, endpoint via MEMORAY_BASE_URL or the wizard manifest):

• Page — #/_prime_silo/memory: Command Center cards, session list, lineage graph, node inspector, a conformance strip, and first-class offline/disabled screens.
• Agent skill — memory-recall: the onscreen agent answers "what was I working on / which sessions touched file X" by querying the graph itself.
• CLI — node space memory <status|sync|sessions|search|audit>.
• Self-audit — the integration is declared in manifests/integrations/memoray.integration.json (data model + process map + config surface, HMAC-signed). GET /api/integration_audit / node space memory audit / node scripts/audit-integrations.mjs probe live reality against that declaration and emit a drift report whose findings carry the owner path to fix — so an agent (or a local LLM via Lemonade) can maintain it without spelunking. See manifests/integrations/AGENTS.md.

Bridge — one cockpit for the whole mesh

Phase B ropes the scattered pages into a single calm surface at #/_prime_silo/bridge — designed for one mental model, not six tabs. A mode rail (Pulse · Memory · Documents · Code 3D · Flows · Runs), one stage, and Benny (the onscreen agent) in the dock, grounded in whatever's on screen so you can ask "explain this" / "what did I work on" and get a real answer with a deep link back.

• Golden paths, not copy-paste — Flows: type a requirement → Plan renders the DAG → Run flips to live observability. Documents: pick a workspace → manage files → Ingest turns documents into semantic triples (rendered as the knowledge graph) → Correlate links them to the code graph.
• 3D when you want it — Code 3D and the knowledge graph default to an offline-safe 2D layout with a one-click 3D (WebGL) toggle.
• Same thesis — declared as a signed manifest (manifests/integrations/bridge.integration.json) covered by the self-audit, and ubiquitous: page + benny-pilot agent skill + node space bridge <status|plan|run|ingest|open>. Configurable landing via BRIDGE_DEFAULT_MODE. Pulse carries Memo-Ray's /api/lifelog activity feed (sessions + artifacts + git commits).

Repo layout

prime-silo/
├── app/                      # space-agent — browser frontend
├── server/                   # space-agent — thin Node.js shell server
├── space/                    # space-agent — agent runtime
├── packaging/                # space-agent — desktop builds
├── runtime/                  # vendored from skybluecycology/benny
│   ├── benny/                #   FastAPI backend, Pypes, swarm, governance
│   ├── manifests/            #   Pypes/swarm manifests
│   ├── tests/                #   pytest suite (~200 tests)
│   ├── docs/                 #   operator manuals, ADRs, requirements
│   └── architecture/         #   ADR-001 lives here
├── scripts/                  # prime-silo dev/launch scripts
└── README.md                 # this file

Status

• Phase A — agent sandbox boundary, scope guard middleware, widget registry contract, agent-authorship lineage emitter (in runtime/benny/)
• Phase B — fork bootstrap; Benny vendored under runtime/, space-agent shell merged
• Phase C — eight canvases migrated to the shell widget tree (text.markdown, run.reasoning_trace, run.lineage_timeline, run.drilldown_table, run.frame_inspector, kg3d.synoptic_web, codegraph.canvas, dag.canvas)
• Phase D / D2 / D3 — runtime transport, agent-context chokepoint, agent saved-views helpers
• Phase F / F2 / F2b — .aamp.view HMAC sign / verify / pin / load chokepoint; pinned views are self-describing signed JSON, GET /api/views/load/<ws>/<filename> returns {view, signature, valid} in one round-trip
• Phase E — first deterministic-zone shell page (manifest_explorer) lists registered swarm manifests and renders the selected one as dag.canvas. No agent context — runtimeFetch with no scope.
• Phase H1 — session checkpoints: save/restore/fork session state (history + skills + staged data + run refs); draft endpoints under the agent sandbox, human-only HMAC pinning
• Phase M1 — memory graph in-shell: Memo-Ray integration declared as a signed aamp.integration/1 manifest (data model + process map + config surface), surfaced on four surfaces (page #/_prime_silo/memory, memory-recall agent skill, node space memory CLI, /api/integration_audit self-audit) over one configurable proxy
• Phase B (Bridge) — one cockpit (#/_prime_silo/bridge) unifying memory, documents→triples, code, flows and runs with Benny grounded in the stage; signed bridge.integration.json; ubiquitous (page + benny-pilot skill + node space bridge); carries Memo-Ray's lifelog feed
• Phase M2 — LLM self-maintenance loop: a swarm manifest that runs the audit → call_model() (Lemonade local) → drafts fixes into agent_sandbox/drafts/ for human pinning
• Phase G — canvas consolidation; retire ManifestCanvas/PipelineCanvas/WorkflowCanvas duplication in the runtime frontend

Phase status is tracked rolling in architecture/ROADMAP.md. The original phase rationale lives in runtime/architecture/ADR-001-prime-silo-shell-fork.md §8.

Quickstart

# 1. Install Python + Node deps
cd runtime
python -m pip install -e .
cd ..\server
npm install
cd ..

# 2. Set required environment (HMAC key — runtime owns it; browser never sees it)
$env:BENNY_HMAC_KEY = "<64-hex-character key>"   # see OPERATING_MANUAL.md §2.5 for how to generate

# 3. Boot runtime + shell in parallel
.\scripts\dev.ps1                                # bash users: ./scripts/dev.sh

# 4. Verify the ADR-001 surfaces are live
curl http://localhost:8005/api/agent_sandbox/health
curl http://localhost:8005/api/widgets

# 5. Browse manifests in the shell:
#    open http://localhost:3000/#/_prime_silo/manifest_explorer

A full setup-from-scratch walkthrough, including prerequisites, HMAC key generation, smoke tests, and a feature-by-feature usage guide, lives in architecture/OPERATING_MANUAL.md.

Updating the vendored Benny tree

git remote add benny https://github.com/skybluecycology/benny.git   # one-time
git subtree pull --prefix=runtime benny master --squash

Fixes that originate in runtime/ go back upstream as PRs against skybluecycology/benny. Anything touching runtime/benny/ lands upstream first; the fork only owns:

• Space-agent shell customisations
• Migrated React widget components (Phase C onward)
• .aamp.view view bundles
• Fork-specific docs

License

Space-agent shell code under LICENSE (inherited from upstream). The vendored Benny tree retains its own license at runtime/LICENSE where applicable.

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Prime-Silo — engineered by Binary 16.