mkdocs.yml

site_name: Spector Documentation
site_description: "Spector — cognitive memory engine for AI agents. Four-tier store, association-graph recall, sub-millisecond scoring, no external database."
site_url: https://spectrayan.github.io/spector/
repo_url: https://github.com/spectrayan/spector
repo_name: spectrayan/spector
copyright: "Copyright © 2026 Spectrayan — Apache License 2.0"

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    - content.code.copy            # Copy button on code blocks
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    # TOC
    - toc.follow                   # TOC follows scroll position

plugins:
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  - callouts
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hooks:
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# ═══════════════════════════════════════════════════════════════
#  Navigation — organized by user intent, max 3 levels deep
# ═══════════════════════════════════════════════════════════════

nav:
  # Tab 1: First impression — "what is this?"
  - Home:
      - Welcome: index.md
      - "Why Spector?": why-spector.md
      - About: about.md

  # Tab 2: "I want to start using it NOW" (action-oriented)
  - Getting Started:
      - Quick Start: getting-started/quickstart.md
      - Installation: getting-started/installation.md
      - Developer Guide: getting-started/developer-guide.md
      - "JDK API Status": getting-started/jdk-api-status.md
      - MCP Server: sdk-usage/mcp-server.md
      - Java SDK: sdk-usage/java-client.md
      - Java API Reference: apidocs/index.html
      - Python SDK: sdk-usage/python-sdk.md
      - TypeScript SDK: sdk-usage/typescript-sdk.md
      - Spring AI Integration: sdk-usage/spring-ai.md
      - CLI Reference:
          - spector: cli-reference/spector.md
          - spector-inspect: cli-reference/spector-inspect.md
      - REST API: api-reference/rest-endpoints.md
      - "API Playground": api-reference/playground.md
      - Error Codes: api-reference/error-codes.md
      - Configuration:
          - Overview & Precedence: configuration/index.md
          - spector.yml Reference: configuration/spector-yml.md
          - Environment Variables & Secrets: configuration/environment-variables.md
          - Deployment & Cloud Config: configuration/deployment-config.md
          - REST API & Runtime Parameters: configuration/api-parameters.md
          - Engine & Algorithmic Tuning: configuration/parameters.md
      - Deployment:
          - Docker & Compose: deployment/docker.md
          - Kubernetes & Helm: deployment/helm.md
          - Terraform Cloud Modules: deployment/terraform.md
          - Disaster Recovery Runbook: operations/disaster-recovery.md
          - "Observability & Metrics": operations/observability.md

  # Tab 3: Cognitive Memory — the differentiator (own tab)
  - Cognitive Memory:
      - Overview: memory/index.md
      - Getting Started: memory/getting-started.md
      - Use Cases: memory/use-cases.md
      - API Reference: memory/api-reference.md
      - Concepts:
          - Four memory tiers: memory/tiers.md
          - Recall scoring: memory/scoring-pipeline.md
          - Scoring regimes: memory/scoring-regimes.md
          - Association graph: memory/association-graph.md
          - Retrieval stack:
              - Overview: memory/retrieval-overview.md
              - Keyword (BM25): memory/bm25.md
              - Learned sparse (SPLADE): memory/splade.md
              - Late interaction (ColBERT): memory/colbert.md
      - Pathways:
          - Remember, Recall, Reflect: memory/architecture.md
          - Offline consolidation: memory/consolidation.md
      - Scoring features:
          - Tags and Bloom gating: memory/tags.md
          - Valence: memory/valence.md
          - Novelty detection: memory/novelty.md
          - Habituation: memory/habituation.md
          - Inhibition: memory/inhibition.md
          - Dedup and interference: memory/interference.md
          - Importance fusion: memory/importance-fusion.md
          - Salience profiles: memory/salience-importance.md
      - Profiles:
          - Overview: memory/cognitive-profiles.md
          - Self-tuning adaptor: memory/profile-adaptor.md
          - Focus mode: memory/focus-mode.md
          - Explorer (lateral retrieval): memory/lateral-retrieval.md
      - Experimental:
          - Overview: memory/experimental.md
          - AISME (persona and affect): memory/aisme.md
          - Dream: memory/dreaming.md
          - Wander: memory/wander.md
          - Decide: memory/decide.md
          - Express: memory/express.md
          - Constructive simulation: memory/constructive-memory.md
          - Prospective intents: memory/prospective.md
          - Metamemory: memory/metamemory.md
      - Internals:
          - Architecture: memory/architecture.md
          - Performance and SIMD: memory/performance.md
          - Off-heap Panama: memory/panama-design.md
          - WAL: memory/wal-design.md
          - Bundle format compatibility: memory/bundle-format-compatibility.md
          - Sync and replication: memory/sync.md
          - Evaluation: memory/evaluation.md
      - Design ancestry: memory/theoretical-foundations.md

  # Tab 4: Memory Kernel — zero-GC Panama FFM storage backbone (NEW TAB!)
  - "Memory Kernel":
      - Overview: kernel/index.md
      - "Bundle Architecture": kernel/bundles.md
      - "Memory Shapes": kernel/shapes.md
      - "Binary Layouts & Tags": kernel/layouts.md
      - "WAL & Durability": kernel/wal-recovery.md
      - "Region Reference":
          - "Overview & Index": kernel/regions/index.md
          - "Partition Regions":
              - "Semantic Memory": kernel/regions/semantic.md
              - "Episodic Memory": kernel/regions/episodic.md
              - "Procedural Memory": kernel/regions/procedural.md
              - "Text Blob Store": kernel/regions/text.md
              - "Strength State": kernel/regions/strength.md
          - "Runtime Regions":
              - "Working Memory": kernel/regions/working.md
              - "Co-Activation Matrix": kernel/regions/coactivation.md
              - "Index MIDX": kernel/regions/index-midx.md
              - "Index IDPL": kernel/regions/index-idpl.md
              - "Hebbian Graph": kernel/regions/hebbian.md
              - "Temporal Chains": kernel/regions/temporal-chain.md
              - "Temporal Facts": kernel/regions/temporal-facts.md
              - "Entity Directory": kernel/regions/entity-directory.md
              - "Entity Names Pool": kernel/regions/entity-names.md
              - "HyperEntity Graph": kernel/regions/hypergraph.md
              - "Entity Types Registry": kernel/regions/entity-types.md
              - "Relation Types Registry": kernel/regions/relation-types.md
              - "BM25 Lexical Index": kernel/regions/bm25.md
              - "Checkpoint": kernel/regions/checkpoint.md
              - "Insula (Somatic Self-Model)": kernel/regions/insula.md
              - "Continuity": kernel/regions/continuity.md
              - "Provenance": kernel/regions/provenance.md
              - "SPLADE Sparse Index": kernel/regions/splade.md
              - "Entity Reverse Index": kernel/regions/entity-reverse-index.md
          - "Identity Regions":
              - "Identity Header": kernel/regions/identity-header.md
              - "Soul Context": kernel/regions/soul.md
              - "Salience Profile": kernel/regions/salience.md
              - "Identity Continuity": kernel/regions/identity-continuity.md
              - "Governance Policy": kernel/regions/policy.md
              - "Org Directory": kernel/regions/org-dir.md

  # Tab 5: Synapse & Cortex — the agentic layer (own tab)
  - "Synapse & Cortex":
      - "Synapse Overview": synapse/index.md
      - "Cortex Dashboard & Chat": cortex/index.md

  # Tab 6: Architecture & Modules
  - Architecture:
      - System Overview: architecture/overview.md
      - Core Concepts: architecture/core-concepts.md
      - Ingestion Pipeline: architecture/ingestion-pipeline.md
      - MCP Integration: architecture/mcp-integration.md
      - Distributed Mode: architecture/distributed-mode.md
      - Event Notifications: architecture/event-notifications.md
      - Namespace Sharding: architecture/namespace-sharding.md
      - "Single-Namespace Scale & Capacity Limits": capacity/single-namespace-scale.md
      - "Scale Benchmark Empirical Results": capacity/scale-benchmark-results.md
      - "Writer Quiesce Pause Empirical Results": capacity/quiesce-pause-benchmark-results.md
      - "Kill-Owner Failover Empirical Results": capacity/kill-owner-recovery-results.md
      - "Salience & Importance Architecture": architecture/salience-importance.md
      - GPU Acceleration: architecture/gpu-acceleration.md
      - Performance Tuning: operations/performance-tuning.md
      - Test Framework & LLM Judge: architecture/test-framework.md
      - "Chat & Visual Test Infrastructure": architecture/test-infrastructure.md
      - Security & Data:
          - "Encryption at Rest": architecture/encryption-at-rest.md
      - "Architecture Decision Records (ADRs)":
          - Overview: adr/README.md
          - Template: adr/0000-template.md
          - "Master Catalog (0001-0085)": adr/catalog.md
          - "Memory Kernel & Storage Formats":
              - "ADR-0001: Graph Compression Strategy for Entity Graph": adr/0001-graph-compression-strategy.md
              - "ADR-0002: Multi-Partition Recall Fan-Out & Frozen Reten...": adr/0002-multi-partition-recall-fanout.md
              - "ADR-0003: Completing Hypergraph Entity-Graph Graduation": adr/0003-hypergraph-entity-graph-graduation.md
              - "ADR-0004: Mmap Bundle Architecture & File Descriptor Sc...": adr/0004-mmap-bundle-architecture-and-fd-scaling.md
              - "ADR-0005: spector-memory Technical Debt Hardening": adr/0005-spector-memory-technical-debt-hardening.md
              - "ADR-0042: Graph Recall Architecture and Cognitive Trave...": adr/0042-graph-recall-architecture-and-cognitive-traversals.md
              - "ADR-0043: Single-VMA Bundle Layout Specification": adr/0043-single-vma-bundle-layout-specification.md
              - "ADR-0044: Memory Kernel Isolation, Composition, and Layout": adr/0044-memory-kernel-isolation-and-layout.md
              - "ADR-0045: Spector Memory Import & Export Pipeline": adr/0045-spector-memory-import-export-pipeline.md
              - "ADR-0046: Single Engram, Four Stores Storage Architecture": adr/0046-single-engram-storage-architecture.md
              - "ADR-0047: Episodic Memory and Engram Model Hierarchy": adr/0047-episodic-memory-and-engram-model.md
              - "ADR-0057: Remediation of Hardcoded Memory Offsets and Alignment Constants": adr/0057-hardcoded-memory-offsets-and-alignment-constants.md
              - "ADR-0062: Spector Memory Organization — Three-Plane Architecture": adr/0062-memory-organization-three-plane-architecture.md
              - "ADR-0082: Index Plane Lifecycle, Derived Views, and Reconciliation": adr/0082-index-plane-lifecycle-and-derived-view-reconciliation.md
          - "Active Inference Self-Model Engine (AISME)":
              - "ADR-0006: Episodic Conversation Architecture": adr/0006-episodic-conversation-architecture.md
              - "ADR-0007: ReflectPathway — Biological Sleep Consolidation": adr/0007-reflect-pathway-sleep-consolidation.md
              - "ADR-0008: Cognitive Substrate Evolution (TANGLE, GPM, M...": adr/0008-cognitive-substrate-evolution-tangle-gpm-msce.md
              - "ADR-0009: AISME Phase 1 — Homeostatic Affective Core": adr/0009-aisme-phase-1-homeostatic-affective-core.md
              - "ADR-0010: AISME Phase 2 — Free-Energy Guided Recall": adr/0010-aisme-phase-2-free-energy-guided-recall.md
              - "ADR-0011: AISME Phase 3 — Modern Hopfield Associative M...": adr/0011-aisme-phase-3-modern-hopfield-associative-memory.md
              - "ADR-0012: AISME Phase 4 — Neural Manifold Distance (NMD)": adr/0012-aisme-phase-4-neural-manifold-distance.md
              - "ADR-0013: AISME Phase 5 — Predictive Coding Narrative Self": adr/0013-aisme-phase-5-predictive-coding-narrative-self.md
              - "ADR-0014: AISME Phase 6 — Consciousness Continuity Metr...": adr/0014-aisme-phase-6-consciousness-continuity-metric.md
              - "ADR-0015: AISME Phase 7 — Synaptic Relay Wiring & Pathw...": adr/0015-aisme-phase-7-synaptic-relay-wiring.md
              - "ADR-0016: AISME Phase 8 — Closed-Loop Epistemic Learning": adr/0016-aisme-phase-8-closed-loop-epistemic-learning.md
              - "ADR-0017: AISME Phase 9 — Generative Counterfactuals & ...": adr/0017-aisme-phase-9-generative-counterfactuals-prior-plasticity.md
              - "ADR-0018: AISME Phase 10 — WanderPathway & Kernel Conti...": adr/0018-aisme-phase-10-wander-pathway-continuity-mmap-layout.md
              - "ADR-0019: AISME Phase 11 — Expected Free Energy Policy ...": adr/0019-aisme-phase-11-expected-free-energy-policy-engine.md
              - "ADR-0020: AISME Phase 12 — Continuous Self-Dynamics": adr/0020-aisme-phase-12-continuous-self-dynamics.md
              - "ADR-0023: AISME Complete Loop Closure & CognitiveVector...": adr/0023-aisme-loop-closure-and-cognitive-vector-accessor.md
              - "ADR-0024: Polymorphic SoulContext Hierarchy in AISME": adr/0024-polymorphic-soul-context-aisme.md
              - "ADR-0027: Soul-Conditioned & Salience-Modulated Persona...": adr/0027-soul-conditioned-personalized-dreaming.md
              - "ADR-0048: Cross-Capture Graph & CoActivation Kernel": adr/0048-cross-capture-graph-coactivation-kernel.md
              - "ADR-0049: Identity Trajectory Lyapunov Stability": adr/0049-identity-trajectory-lyapunov-stability.md
              - "ADR-0050: Event Density Gating and Dynamic Epistemic Co...": adr/0050-event-density-gating-epistemic-compression.md
              - "ADR-0051: Bayesian Online Change-Point Episode Segmenta...": adr/0051-bayesian-online-changepoint-episode-segmentation.md
              - "ADR-0052: Differential Privacy and Edge Anonymization": adr/0052-differential-privacy-edge-anonymization.md
              - "ADR-0053: Multimodal Composite Importance Scoring": adr/0053-multimodal-composite-importance-scoring.md
              - "ADR-0054: Lifespan-Adaptive Forgetting & Retention Kernel": adr/0054-lifespan-adaptive-forgetting-retention.md
              - "ADR-0055: LSR & RFF Dense Associative Memory Engineerin...": adr/0055-lsr-rff-associative-memory-engineering-specification.md
              - "ADR-0056: Log-Sum-ReLU (LSR) & Random Fourier Features ...": adr/0056-lsr-rff-dense-associative-memory.md
              - "ADR-0058: Linguistic & Vocal Prosody Expression Engine": adr/0058-linguistic-vocal-prosody-expression-engine.md
              - "ADR-0063: Spacetime Vector Search and Synaptic Relay Architecture": adr/0063-spacetime-vector-search-synaptic-relay-architecture.md
              - "ADR-0064: Spacetime Simulation on Wander, Dream, and Express Pathways": adr/0064-spacetime-simulation-wander-dream-express.md
              - "ADR-0071: Remember Cognitive Pathway Architecture": adr/0071-remember-cognitive-pathway-architecture.md
              - "ADR-0072: Six-Phase Fused Cognitive Scoring Pipeline": adr/0072-six-phase-fused-cognitive-scoring-pipeline.md
              - "ADR-0073: Recall Cognitive Pathway and Multi-Phase Retrieval Architecture": adr/0073-recall-cognitive-pathway-multi-phase-retrieval.md
              - "ADR-0074: Reflect Cognitive Pathway and Sleep Consolidation Architecture": adr/0074-reflect-cognitive-pathway-sleep-consolidation.md
              - "ADR-0078: Salience Network and Thalamic Cognitive Profiles Architecture": adr/0078-salience-network-and-thalamic-cognitive-profiles.md
          - "Platform, Synapse & Clustering":
              - "ADR-0021: Nucleus Symmetric Hardware Abstraction Layer ...": adr/0021-nucleus-symmetric-hardware-abstraction-layer.md
              - "ADR-0022: Embodied Kinesics & Phenomenological MCP Engine": adr/0022-embodied-kinesics-phenomenological-mcp-engine.md
              - "ADR-0025: Declarative MCP Tool Definitions via JSON Sch...": adr/0025-declarative-mcp-tool-definitions.md
              - "ADR-0026: Dual-Plane Concurrency & Async Queue Backpres...": adr/0026-dual-plane-concurrency-and-backpressure.md
              - "ADR-0028: Dual-Plane Memory Audit Architecture (Separat...": adr/0028-dual-plane-memory-audit-architecture.md
              - "ADR-0029: Episodic→Semantic Lineage Provenance Region": adr/0029-episodic-semantic-lineage-provenance-region.md
              - "ADR-0030: Unified Engram Encoding Header Architecture": adr/0030-unified-engram-encoding-header-architecture.md
              - "ADR-0031: Unified Configuration Architecture & Bypass E...": adr/0031-unified-configuration-architecture.md
              - "ADR-0032: Persona Enactment — Soul as Policy over Memory": adr/0032-persona-enactment.md
              - "ADR-0033: Decoupling Cognitive & Mathematical Kernels t...": adr/0033-cognitive-and-mathematical-kernel-decoupling-to-spector-core.md
              - "ADR-0034: Cell Topology, Namespace Ownership, and HA Cl...": adr/0034-cell-ha-namespace-ownership.md
              - "ADR-0035: Cognitive Pathway Framework Rearchitecture": adr/0035-cognitive-pathway-rearchitecture.md
              - "ADR-0036: Pathway Error Handling, Isolation, and Circui...": adr/0036-pathway-error-handling-and-circuit-breakers.md
              - "ADR-0037: Ingestion Boundary and Sensory Relocation": adr/0037-ingestion-boundary-and-sensory-relocation.md
              - "ADR-0038: SIMD-Accelerated BM25 Lexical Scoring Optimiz...": adr/0038-bm25-optimization.md
              - "ADR-0039: Robust Unified Rate Limiting Architecture": adr/0039-robust-unified-rate-limiting-architecture.md
              - "ADR-0040: Universal Apache Camel Messaging Channels": adr/0040-universal-camel-messaging-channels.md
              - "ADR-0041: Unified Connector Architecture for Ingestion": adr/0041-connector-architecture-unification.md
              - "ADR-0059: Java 27 Upgrade Strategy and Value Class Migration": adr/0059-jdk27-upgrade-and-feature-architecture.md
              - "ADR-0060: Cognitive Continuity Layer and Decoded Mind Streams": adr/0060-cognitive-continuity-decoded-mind-streams.md
              - "ADR-0061: In-Memory Multi-Tenant Quartz Scheduler": adr/0061-in-memory-multi-tenant-quartz-scheduler.md
              - "ADR-0065: Client SDK Architecture, OpenAPI, and MCP Integration": adr/0065-client-sdk-openapi-and-mcp-integration-architecture.md
              - "ADR-0066: Engine & CLI Stabilization — Issue #727 Hardening": adr/0066-engine-and-cli-stabilization.md
              - "ADR-0067: Cell-Based High Availability and Namespace-Sticky Sharding": adr/0067-cell-ha-namespace-sticky-sharding.md
              - "ADR-0068: Phileas PII Redaction Engine for Spector Synapse": adr/0068-phileas-pii-engine-for-spector-synapse.md
              - "ADR-0069: Synapse-Owned Tool Access Policy": adr/0069-synapse-owned-tool-access-policy.md
              - "ADR-0070: Unified Error Taxonomy and Exception Handling Architecture": adr/0070-unified-error-taxonomy-and-exception-handling.md
              - "ADR-0075: Extensible LLM and Multimodal Embedding Provider SPI": adr/0075-extensible-llm-and-embedding-provider-spi.md
              - "ADR-0076: Zero-Dependency Pluggable Cache Abstraction": adr/0076-zero-dependency-pluggable-cache-abstraction.md
              - "ADR-0077: Model B Asynchronous Task Queue and Concurrency": adr/0077-model-b-asynchronous-task-queue-concurrency.md
              - "ADR-0079: Asynchronous Memory Event and Telemetry Notification Bus": adr/0079-memory-event-and-telemetry-notification-bus.md
              - "ADR-0080: Observed Memory and Pathway Metrics Telemetry Architecture": adr/0080-observed-memory-and-pathway-metrics-telemetry.md
              - "ADR-0081: Dedicated Reactive Ingress and In-Process Path Router": adr/0081-dedicated-reactive-cell-ingress-router.md
              - "ADR-0083: Namespace-Isolated Memory Analytics & Telemetry": adr/0083-namespace-isolated-memory-analytics-telemetry.md
              - "ADR-0084: Dual-Plane Conversation Persistence": adr/0084-dual-plane-conversation-persistence.md
              - "ADR-0085: Dynamic Synapse Configuration Overrides and Runtime Propagation": adr/0085-dynamic-synapse-configuration-and-runtime-propagation.md
      - "Modules Registry":
          - Overview: modules/index.md
          - "Foundation Layer (/nucleus)":
              - spector-bom: modules/spector-bom.md
              - spector-commons: modules/spector-commons.md
              - spector-core: modules/spector-core.md
              - spector-cpu: modules/spector-cpu.md
              - spector-gpu: modules/spector-gpu.md
              - spector-hdc: modules/spector-hdc.md
              - spector-index: modules/spector-index.md
              - spector-config: modules/spector-config.md
              - spector-events: modules/spector-events.md
              - spector-test-support: modules/spector-test-support.md
          - "Cognitive Layer (/memory)":
              - spector-kernel: modules/spector-kernel.md
              - spector-memory: modules/spector-memory.md
              - spector-provider-api: modules/spector-provider-api.md
              - spector-providers: modules/spector-providers.md
              - spector-ingestion: modules/spector-ingestion.md
              - spector-inspect: modules/spector-inspect.md
              - spector-metrics: modules/spector-metrics.md
          - "Gateway Layer (/synapse)":
              - spector-synapse: modules/spector-synapse.md
              - spector-connector: modules/spector-connector.md
              - spector-mcp: modules/spector-mcp.md
              - spector-mel: modules/spector-mel.md
              - spector-cli: modules/spector-cli.md
              - spector-spring: modules/spector-spring.md
              - spector-batch: modules/spector-batch.md
          - "Benchmarks & UI":
              - spector-bench: modules/spector-bench.md
              - spector-cortex: modules/spector-cortex.md
      - Deep Dives:
          - ANN Search Primer: deep-dives/ann-search-primer.md
          - HNSW Explained: deep-dives/hnsw-explained.md
          - SpectorIndex Architecture: deep-dives/spector-index-architecture.md
          - "Provenance Region": deep-dives/provenance-region.md
          - SVASQ Quantization: deep-dives/svasq-deep-dive.md
          - Understanding Quantization: deep-dives/understanding-quantization.md
          - Quantization Comparison: deep-dives/quantization-comparison.md
          - TurboQuant: deep-dives/turbo-quant.md
          - Real-Embedding Benchmarks: deep-dives/real-embedding-benchmarks.md
          - "Whitepaper: SVASQ + SpectorIndex": deep-dives/svasq-spectorindex-whitepaper.md

  # Tab 7: Community & Labs
  - Community:
      - Governance: community/governance.md
      - Contributing: operations/contributing.md
      - FAQ: faq.md
      - Glossary: glossary.md
      - Roadmap: roadmap.md
      - "🔬 Labs":
          - labs/index.md
          - Research Roadmap: labs/roadmap.md
          - "Hyperdimensional Computing": labs/hdc.md
      - "Third-Party Legal":
          - "DejaVu Fonts": apidocs/legal/dejavufonts.md
          - "jQuery": apidocs/legal/jquery.md
          - "jQuery UI": apidocs/legal/jqueryUI.md

# ═══════════════════════════════════════════════════════════════
#  SEO & Social
# ═══════════════════════════════════════════════════════════════

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/spectrayan/spector
  # Analytics (uncomment when ready)
  # analytics:
  #   provider: google
  #   property: G-XXXXXXXXXX
  generator: false              # Remove "Made with Material for MkDocs" footer

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/mermaid-zoom.js
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
  - javascripts/fluid-transitions.js