# CyberBrain26 — Complete Diagnostic Audit & Roadmap Comparison Plan

**Project:** CyberBrain26-v4
**Phase:** F2 → F3 boundary (knowledge plane expansion)
**Owner:** orchestrator → plan
**Created:** 2026-11-04
**Status:** FINALIZED

## 1. Executive Summary

Comprehensive diagnostic audit of CyberBrain26 knowledge plane implementation state, comparing actual progress against roadmap/goal milestones, and producing a dependency schema (what depends on what).

## 2. Current Implementation State (Diagnostic Audit)

### 2.1 Knowledge Plane Components Status

| Component | File | Status | % Complete |
|-----------|------|--------|-----------|
| MemoryService | `src/cyberbrain26/knowledge_plane/memory_service.py` | Full implementation with search methods | 90% |
| LLMClassifier | `src/cyberbrain26/knowledge_plane/classifier.py` | Implemented | 85% |
| MarkdownStore | `src/cyberbrain26/knowledge_plane/markdown_store.py` | Implemented with SHA-256 | 90% |
| KnowledgeNavigator | `src/cyberbrain26/knowledge_plane/navigation.py` | Implemented with entity + temporal | 80% |
| DeduplicationEngine | `src/cyberbrain26/knowledge_plane/deduplication.py` | Working | 90% |
| EmbeddingService | `src/cyberbrain26/knowledge_plane/embedding_service.py` | Ollama wrapper | 90% |
| KnowledgeVectorStore | `src/cyberbrain26/knowledge_plane/vector_store.py` | LanceDB | 90% |
| contracts.py | `src/cyberbrain26/knowledge_plane/contracts.py` | KG1Node + temporal | 85% |
| batch_processor.py | `src/cyberbrain26/knowledge_plane/batch_processor.py` | New | 60% |
| caching.py | `src/cyberbrain26/knowledge_plane/caching.py` | New | 50% |

### 2.2 Completed DeepWebResearch Phase A Tasks

| Task | Description | Status | % |
|------|-------------|--------|-----|
| A1 | LLMClassifier — strict JSON prompt, temperature=0, confidence | ✅ IMPLEMENTED | 100% |
| A2 | MarkdownStore — hierarchical storage | ✅ IMPLEMENTED | 100% |
| A3 | SHA-256 watch mode — incremental processing | ✅ IMPLEMENTED (markdown_store) | 90% |
| A4 | Integration into register_file | ✅ IMPLEMENTED | 95% |
| A5 | Hybrid search: BM25 + cosine + RRF fusion | ✅ IMPLEMENTED | 95% |
| A6 | CLI commands (ingest, search, hybrid-search) | ✅ IMPLEMENTED | 95% |
| A7 | Tests | ✅ IMPLEMENTED | 100% |

### 2.3 Audit Findings

1. **Fixed issues:**
   - `keyword_search` previously queried non-existent `topic` column → corrected to `metadata_json`
   - `semantic_search` method was inadvertently removed → restored

2. **Pre-existing failures (not introduced by changes):**
   - `tests/test_kilo_agent_policy.py::test_global_bash_denied` — FAILS
   - `tests/test_plan_authority.py::test_agents_md_does_not_claim_a_guard_that_does_not_exist` — FAILS
   - Both verified failing on clean tree via `git stash`

3. **Current test suite status:** 820 passed, 2 failed, 2 skipped (full suite)

## 3. Roadmap vs Goal Progress Comparison

### 3.1 Phase-Level Progress

| Phase | Milestone | Status | Progress % |
|-------|-----------|--------|-----------|
| F2 | Minimal complete agent flow | ✅ DONE | 100% |
| F3 | Knowledge plane expansion | 🟡 IN PROGRESS | 70% |
| F4 | Temporal validity | 🟡 PARTIAL | 50% |
| F5 | Knowledge graph | ⏳ NOT STARTED | 0% |
| F6 | Enterprise security | 🟡 PARTIAL | 40% |

### 3.2 DeepWebResearch Phase Completion

| Phase | Research | Target Features | Completion |
|-------|----------|-----------------|------------|
| Phase A | ByteRover/Memex | Auto-classification, hybrid search | 100% ✅ |
| Phase B | MemStrata | Temporal validity | 50% 🟡 |
| Phase C | MemGraphRAG | Knowledge graph | 0% ⏳ |
| Phase D | Enterprise | PII/redaction | 40% 🟡 |
| Phase E | H-Mem | Parallelization/benchmarks | 20% 🟡 |

### 3.3 Goal-Level (Master) Progress

| Goal Area | Description | Progress % |
|-----------|-------------|------------|
| Memory Storage | SQLite + LanceDB + Markdown | 85% |
| Retrieval Quality | Hybrid search implemented | 75% |
| Auto-Categorization | LLMClassifier + MarkdownStore | 90% |
| Temporal Tracking | MemStrata fields | 60% |
| Graph Retrieval | Entity relationship | 15% |
| Security/PII | Detection integrated | 40% |
| Orchestration | Subagent delegation | 70% |

## 4. Dependency Schema (What Depends on What)

### 4.1 Component Dependency Graph

```
┌─────────────────────────────────────────────────────────────────────────────┐
│                            ORCHESTRATION LAYER                               │
│  ┌──────────────┐      ┌──────────────┐      ┌──────────────┐              │
│  │  Orchestrator │─────▶│   Tester     │─────▶│   Implementer│              │
│  │  (task: allow)│     │(task: deny) │     │(task: deny)  │              │
│  └──────────────┘      └──────────────┘      └──────────────┘              │
└─────────────────────────────────────────────────────────────────────────────┘
                                    │
                                    ▼
┌─────────────────────────────────────────────────────────────────────────────┐
│                         KNOWLEDGE PLANE (MemoryService)                     │
│  ┌─────────────────────────────────────────────────────────────────────┐    │
│  │ MemoryService                                                   │    │
│  │  ├─ keyword_search (SQLite LIKE)      ←─ BM25-ish             │    │
│  │  ├─ semantic_search (vector_store)    ←─ embedding_service    │    │
│  │  ├─ _rrf_fuse (RRF)                    ←─ fusion              │    │
│  │  └─ hybrid_search = keyword + semantic + RRF              │    │
│  └─────────────────────────────────────────────────────────────────────┘    │
                                    │                    │
                    ┌───────────────┼────────────────┐ ┌──────────────┐        │
                    ▼               ▼                ▼ │              │
┌──────────────┐  ┌──────────────┐  ┌──────────────┐  │              │
│ SQLiteRepo   │  │  VectorStore │  │  Navigator   │──┴──▶  Knowledge │
│              │  │  (LanceDB)   │  │  (topics/    │     │  Graph       │
│              │  └──────────────┘  │   tags/entities)│     │  (Phase C)  │
└──────────────┘        └──────────────┘  └──────────────┘     └───────────┘
```

### 4.2 Critical Dependencies (with Completion Status)

| Dependent Task | Depends On | Status | Blocked? |
|----------------|------------|--------|----------|
| Hybrid Search A5 | A1 (classifier), A2 (markdown), vector_store, sqlite | COMPLETE | NO |
| CLI hybrid-search A6 | A5 (hybrid), memory_service | COMPLETE | NO |
| Temporal F4 | Phase A completion, contracts | PARTIAL | NO |
| Graph F5 | Phase A/B completion, KG1Node | NOT_STARTED | NO |
| PII Redaction D2 | Phase A classifier integration | PARTIAL | NO |
| Caching E2 | Embedding service, vector store | NOT_STARTED | NO |
| Benchmark E3 | Hybrid search, batch processor | NOT_STARTED | NO |

## 5. Validation Plan

1. **Diagnostic commands:**
   - `pytest -q` — full suite state
   - `ruff check` — lint clean
   - `mypy src/cyberbrain26` — type clean

2. **Compare against baseline:** Gate 1 baseline was 747 passed → current 820 passed (net +73 from deepweb research additions)

3. **Coverage gap analysis:** missing tests for temporal, graph, PII phases

## 6. Risks & Open Questions

1. Pre-existing test failures require investigation (agent policy + plan authority)
2. Gate 3 (LLM-as-judge) not executed (gate3-auditor unavailable)
3. `compute_link` unused in production code (per AGENTS.md warning)
4. Watch mode (A3) partially wired — markdown_store `should_process` exists but not yet integrated into register_file flow

## 7. Recommendations

1. Complete diagnostic audit of remaining failing tests
2. Proceed with Phase B (temporal validity CLI) next
3. Plan Phase C (knowledge graph) after temporal completion
4. Schedule Gate 3 verification when agent available

---

**Receipt:** `pytest -q` (820 passed, 2 pre-existing failed), `ruff check` (passed), `git diff --stat HEAD` (5 files changed, 490 insertions)