18. Appendix

18.1. Environment variables

Variable	Default	Used by	Effect
EIGENIUS_DB	(none, in-memory)	eigenius serve	Path to the RocksDB persistence directory
EIGENIUS_HOME	workspace root in dev / /opt/eigenius in containers	eigenius env build	Base path for resolving the default Julia worker source ($EIGENIUS_HOME/julia/runtime-worker/). Overridden per invocation by --worker-source-dir.
EIGENIUS_ORCHESTRATOR_ENDPOINT	(none)	eigenius serve	Kernel’s URL for the orchestrator (alternative to --orchestrator)
EIGENIUS_KERNEL_ENDPOINT	http://localhost:50051	Orchestrator	Endpoint the orchestrator uses for kernel callbacks (read/query host imports)
EIGENIUS_ORCHESTRATOR_PORT	8080	Orchestrator	Port the orchestrator binds to
EIGENIUS_MOCK_LLM	false	Orchestrator	When true, swap real LLM handlers for canned mock responses
ANTHROPIC_API_KEY	(none)	Orchestrator	Required when EIGENIUS_MOCK_LLM is unset
RUSTFLAGS	(none)	cargo	RUSTFLAGS="-D warnings" upgrades clippy warnings to errors (used by just check)

CLI commands also accept --endpoint <url> as an alternative to setting an env var; the flag takes precedence.

18.2. File and directory locations

Location	Contents
target/debug/	Workspace build artifacts (debug profile)
target/debug/eigenius	The CLI binary
target/release/	Workspace build artifacts (release profile)
examples/wasm-*/target/wasm32-unknown-unknown/debug/*.wasm	WASM example binaries
kernel/tests/fixtures/*.wasm	Test fixtures copied from WASM examples
~/.cache/deno/	Deno-cached TypeScript dependencies
<rocksdb-path>/ (e.g. /var/lib/eigenius)	Persisted state when serve --db is used
/var/lib/eigenius/substrate-depot/	Runtime-substrate depot path (chapter 11). Bind-mounted into the orchestrator at the same path so worker UDS sockets are reachable from both host and orchestrator container.
julia/runtime-worker/	Julia worker source baked into substrate env images
julia/common/EigeniusJuliaCommon/	Substrate-side Julia utilities shared across institutions
julia/institutions/<institution>/	Per-institution handler package (Project.toml + src/) and chain declarations
julia/comorphisms/	Cross-institution comorphism declarations

18.3. Default ports

Port	Service	Configuration
50051	Kernel gRPC	eigenius serve --port <N>
8080	Orchestrator HTTP	EIGENIUS_ORCHESTRATOR_PORT=<N>

18.4. The four embedded ontology layers

Loaded at every kernel startup; their parent-pointer chain forms the bootstrap:

Layer	IRI base	Source
core	urn:eigenius:core	ontologies/core/core-ontology.json
program	urn:eigenius:program	ontologies/program/program-ontology.json
reflection	urn:eigenius:reflection	(embedded — reasoning traces, epistemic categories)
institution	urn:eigenius:institution	(embedded — institution and comorphism classes)

When serve --db <path> is used, a SHA-256 manifest of these is written on first start and verified on subsequent starts (drift refusal — see chapter 6 §6.3).

18.5. Source index — implementation files referenced in this guide

CLI

• cli/src/main.rs — every subcommand, the Commands enum is the source of truth for command shapes

Kernel

• kernel/src/server/ — gRPC service definitions
• kernel/src/bootstrap/ — embedded ontology loader
• kernel/src/storage/ — storage interface traits
• kernel/src/capability/ — WASM capability hosting; wasm_institution_d14.rs is the host bridge for D14 institutions; registration.rs does chain-scan auto-registration
• kernel/src/institution/runtime.rs — D14 Institution trait, InstitutionRuntime
• kernel/src/institution/registry.rs — InstitutionIndex (derived from chain scan)

Storage backends

• storage/memory/ — in-memory backend (default for serve without --db)
• storage/rocksdb/ — RocksDB backend (serve --db)
• storage/tikv/ — TiKV backend (placeholder)
• kernel/src/layer/index.rs — per-layer triple index trait + in-memory impl (Phase 14h)
• storage/rocksdb/src/triple_index.rs — RocksDB-backed triple index (Phase 14h)

WASM runtime and SDK

• crates/wasm-runtime/ — Wasmtime integration, fuel/memory limits
• sdk/wasm-sdk/ — Rust SDK for authoring components and institutions
• wit/eigenius-component.wit — WIT interface contracts

Runtime substrate (chapter 11)

• crates/runtime-substrate/ — substrate hosting layer (loaded into the orchestrator)
• crates/runtime-substrate/src/language_runtime.rs — LanguageRuntime trait
• crates/runtime-substrate/src/spawner/ — container lifecycle
• crates/runtime-substrate/src/image_build/ — buildah-driven env image construction
• crates/runtime-substrate/src/rpc/ — Eigon-CBOR-over-UDS protocol
• crates/runtime-substrate/src/mirror_generator.rs — closure walker for chain shapes
• crates/eigenius-julia/ — Julia v1 instantiation of LanguageRuntime
• julia/runtime-worker/ — Julia worker (PID 1 in env images)
• julia/institutions/ — five v1 Julia institutions (Symbolics, IntervalArithmetic, Catalyst, DiffEq, JuMP-HiGHS)
• julia/comorphisms/ — cross-institution comorphism declarations

Examples

• examples/wasm-cbor-echo/ — minimum viable component
• examples/wasm-doc-validator/ — pure component with typed I/O
• examples/wasm-read-query-probe/ — read-capability component
• examples/wasm-http-shout/ — IO component dispatching CompleteText
• examples/wasm-d14-echo/ — minimum-viable D14 institution (smoke test of the WIT bindings)
• examples/wasm-d14-dock/, examples/wasm-d14-assay/, examples/wasm-d14-arrhenius/ — the M8 worked example (dock institution + assay institution + Arrhenius transformation Component)

Orchestrator

• orchestration/src/main.ts — entry point, registry setup
• orchestration/src/components/ — CompleteText, CompleteJson, registry
• orchestration/src/llm/adapter.ts — Anthropic adapter
• orchestration/src/mcp/server.ts — MCP tool surface
• orchestration/src/wasm/ — WASM addon hosting (IO components)

Demo scripts

• demo/run.sh — basic document demo
• demo/patent/run.sh — patent analysis pipeline
• demo/wasm/run.sh — WASM extensibility demo

Deployment

• docker-compose.yml — local stack composition
• deploy/Dockerfile.kernel — kernel image
• deploy/Dockerfile.orchestration — orchestrator image
• deploy/bicep/main.bicep — Azure ContainerApps orchestrating template
• deploy/bicep/modules/ — per-resource Bicep modules
• deploy/bicep/parameters/ — staging/production environment overrides

Build / task automation

• justfile — task recipes (build, test, check, up, serve, etc.)

18.6. Related documents

• ESL user guide — the surface language for ontologies and programs
• EigenQL user guide — the query language
• D1 — Eigon serialization format — Eigon-JSON spec
• D2 — EigenQL specification — EigenQL spec
• D6 — Execution architecture — kernel ↔ orchestrator boundary
• D6b — Reasoning trace schema — trace storage
• D7 — ESL surface syntax — ESL spec
• D8 — CompleteJson component — structured LLM output
• D14 — Institution Realisation — institution model (supersedes D10); §9.3 covers comorphism chain reinsertion
• D12 — WASM extensibility — capability levels, host imports, fuel/memory
• D13 — Durable kernel state — serve --db spec, restart re-registration
• D21 — Task traces and checkpointing — task model and resume sweep
• D26 — Runtime substrate — substrate hosting layer, LanguageRuntime trait
• D29 — Mirror generator — closure walker, content-addressed mirror IRIs
• D31 — Runtime-language-substrate institution lifecycle — install flow, env image lifecycle
• D32 — Chain-mirrored EigenTT inductives — formulas:FormulaTerm as a EigenTT fragment on the chain

The full design-document set lives in docs/design/.

18.7. Phase status

The platform is currently complete through Phase 11e (see top-level README.md):

• Phases 0–9: kernel + orchestrator + LLM integration + WASM extensibility + persistence + tasks
• Phase 10: kernel completeness (ontology-as-types resolution)
• Phase 11a–e: type theory extensions (Map/Reduce, inductive types, institution decide procedures, comorphisms, ESL+EigenQL surfaces)

Next: Phase 12 (worked institution examples — life-science demos drawing on Phase 11’s surface).

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