Docs: Add deprecation notice for MCP FAISS+RocksDB architecture

Updated CHANGELOG.md and README.md to clearly communicate the
architectural shift from FAISS+RocksDB to SurrealDB for MCP server
code-agent functionality.

## CHANGELOG.md Updates:

### Added - Unreleased Section:
- Complete documentation of 7 new agentic MCP tools
- Tier-aware orchestration details (Small/Medium/Large/Massive)
- 28 specialized prompts (7 analysis types × 4 tiers)
- Graph analysis integration with 6 SurrealDB tools
- New CLI command: codegraph config agent-status

### Deprecated Section:
- Clear statement: MCP server FAISS+RocksDB support deprecated
- What remains supported: CLI, SDK, NAPI bindings
- Migration path: SurrealDB setup instructions
- Free cloud services highlighted:
  * SurrealDB Cloud: 1GB free instance
  * Jina AI: 10 million free tokens
- Rationale for change explained

## README.md Updates:

### New Section: Important Notice
- Prominent warning about MCP server architecture change
- Clear breakdown of what changed vs. what remains
- Setup requirements for code-agent tools
- Two installation options (cloud vs. local)
- Free resource highlights for both SurrealDB and Jina AI
- Rationale for architectural shift
- Link to CHANGELOG.md for detailed migration guide

### Updated Feature List:
- Added: Agentic code-agent tools with tier-aware reasoning

## Key Messages:

1. **MCP server** deprecates FAISS+RocksDB
2. **CLI/SDK/NAPI** continue to support FAISS+RocksDB
3. **Code-agent tools** require SurrealDB (local or cloud)
4. **Free options available**: 1GB SurrealDB + 10M Jina tokens
5. **Migration is straightforward**: Clear setup instructions provided

This ensures users understand:
- The architectural change and its scope
- What continues to work unchanged
- How to set up new requirements
- Access to free cloud resources
- The technical reasoning behind the change

Author: jruokola

CHANGELOG.md

@@ -5,6 +5,105 @@ All notable changes to the CodeGraph MCP Intelligence Platform will be documente
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - 2025-01-08 - Agentic Code Intelligence & Architecture Migration
+
+### 🚀 **Added - Agentic MCP Tools (AI-Enhanced Feature)**
+
+#### **1. Tier-Aware Agentic Orchestration**
+- **7 Agentic MCP Tools**: Multi-step reasoning workflows for comprehensive code analysis
+  - `agentic_code_search` - Autonomous graph exploration for code search
+  - `agentic_dependency_analysis` - Dependency chain and impact analysis
+  - `agentic_call_chain_analysis` - Execution flow tracing
+  - `agentic_architecture_analysis` - Architectural pattern assessment
+  - `agentic_api_surface_analysis` - Public interface analysis
+  - `agentic_context_builder` - Comprehensive context gathering
+  - `agentic_semantic_question` - Complex codebase Q&A
+- **Automatic tier detection**: Based on LLM context window (Small/Medium/Large/Massive)
+- **Tier-aware prompting**: 28 specialized prompts (7 types × 4 tiers)
+  - Small (<50K): TERSE prompts, 5 max steps, 2,048 tokens
+  - Medium (50K-150K): BALANCED prompts, 10 max steps, 4,096 tokens
+  - Large (150K-500K): DETAILED prompts, 15 max steps, 8,192 tokens
+  - Massive (>500K): EXPLORATORY prompts, 20 max steps, 16,384 tokens
+- **LRU caching**: Transparent SurrealDB result caching (100 entries default)
+- **Configurable max tokens**: `MCP_CODE_AGENT_MAX_OUTPUT_TOKENS` env variable
+
+#### **2. Graph Analysis Integration**
+- **6 SurrealDB graph tools**: Deep structural code analysis
+  - `get_transitive_dependencies` - Full dependency chains
+  - `detect_circular_dependencies` - Cycle detection
+  - `trace_call_chain` - Execution path analysis
+  - `calculate_coupling_metrics` - Ca, Ce, I metrics
+  - `get_hub_nodes` - Architectural hotspot detection
+  - `get_reverse_dependencies` - Change impact assessment
+- **Zero-heuristic design**: LLM infers from structured data only
+- **Tool call logging**: Complete reasoning traces with execution stats
+- **Cache statistics**: Hit rate, evictions, size tracking
+
+#### **3. CLI Enhancements**
+- **New command**: `codegraph config agent-status`
+  - Shows LLM provider, context tier, prompt verbosity
+  - Lists all available MCP tools with descriptions
+  - Displays orchestrator settings (max steps, cache, tokens)
+  - JSON output support for automation
+- **Configuration visibility**: Understand how config affects system behavior
+
+### ⚠️ **Deprecated - MCP Server FAISS+RocksDB Support**
+
+**IMPORTANT**: The MCP server's FAISS+RocksDB graph database solution is now **deprecated** in favor of SurrealDB-based architecture.
+
+**What's Deprecated:**
+- MCP server integration with FAISS vector search
+- MCP server integration with RocksDB graph storage
+- Cloud dual-mode search via MCP protocol
+
+**What Remains Supported:**
+- ✅ **CLI commands**: All FAISS/RocksDB operations remain available via `codegraph` CLI
+- ✅ **Rust SDK**: Full programmatic access to FAISS/RocksDB functionality
+- ✅ **NAPI bindings**: TypeScript/Node.js integration still functional
+- ✅ **Local embeddings**: ONNX, Ollama, LM Studio providers unchanged
+
+**Migration Path:**
+
+For **MCP code-agent** functionality, you must now set up SurrealDB:
+
+**Option 1: Free Cloud Instance (Recommended for testing)**
+1. Sign up at [Surreal Cloud](https://surrealdb.com/cloud) - **FREE 1GB instance included**
+2. Get connection details from dashboard
+3. Configure environment:
+   ```bash
+   export SURREALDB_URL=wss://your-instance.surrealdb.cloud
+   export SURREALDB_NAMESPACE=codegraph
+   export SURREALDB_DATABASE=main
+   export SURREALDB_USERNAME=your-username
+   export SURREALDB_PASSWORD=your-password
+   ```
+
+**Option 2: Local Installation**
+```bash
+# Install SurrealDB
+curl -sSf https://install.surrealdb.com | sh
+
+# Run locally
+surreal start --bind 127.0.0.1:3004 --user root --pass root memory
+
+# Configure
+export SURREALDB_URL=ws://localhost:3004
+export SURREALDB_NAMESPACE=codegraph
+export SURREALDB_DATABASE=main
+```
+
+**Free Cloud Services:**
+- 🆓 **SurrealDB Cloud**: 1GB free instance (perfect for testing and small projects)
+- 🆓 **Jina AI**: 10 million free API tokens when you register at [jina.ai](https://jina.ai)
+  - Includes embeddings, reranking, and token counting APIs
+  - Production-grade embeddings with no local GPU required
+
+**Rationale:**
+- SurrealDB provides native graph capabilities vs. custom RocksDB layer
+- HNSW vector indexing is built-in vs. separate FAISS integration
+- Cloud-native architecture enables distributed deployments
+- Unified storage reduces complexity and maintenance overhead
+
 ## [1.1.0] - 2025-11-08 - Cloud-Native Vector Search & TypeScript Integration
 
 ### 🌟 **Major Release - Cloud Embeddings, Dual-Mode Search, and NAPI Bindings**

README.md

@@ -14,6 +14,49 @@ CodeGraph indexes your source code, creates semantic embeddings, and exposes a *
 - ☁️ **NEW:** Jina AI cloud embeddings with modifiable models and dimensions and reranking
 - 🗄️ **NEW:** SurrealDB HNSW backend for cloud-native and local vector search
 - 📦 **NEW:** Node.js NAPI bindings for zero-overhead TypeScript integration
+- 🤖 **NEW:** Agentic code-agent tools with tier-aware multi-step reasoning
+
+---
+
+## ⚠️ Important: MCP Server Architecture Change
+
+**FAISS+RocksDB support in MCP server is deprecated** in favor of SurrealDB-based architecture.
+
+### What Changed:
+- ❌ **MCP server** no longer uses FAISS vector search or RocksDB graph storage
+- ✅ **CLI and SDK** continue to support FAISS/RocksDB for local operations
+- ✅ **NAPI bindings** still provide TypeScript access to all features
+- 🆕 **MCP code-agent tools** now require SurrealDB for graph analysis
+
+### Required Setup for Code-Agent Tools:
+
+The new agentic MCP tools (`agentic_code_search`, `agentic_dependency_analysis`, etc.) require SurrealDB:
+
+**Option 1: Free Cloud Instance (Recommended)**
+- Sign up at [Surreal Cloud](https://surrealdb.com/cloud)
+- **Get 1GB FREE instance** - perfect for testing and small projects
+- Configure connection details in environment variables
+
+**Option 2: Local Installation**
+```bash
+# Install SurrealDB
+curl -sSf https://install.surrealdb.com | sh
+
+# Run locally
+surreal start --bind 127.0.0.1:3004 --user root --pass root memory
+```
+
+**Free Cloud Resources:**
+- 🆓 **SurrealDB Cloud**: 1GB free instance at [surrealdb.com/cloud](https://surrealdb.com/cloud)
+- 🆓 **Jina AI**: 10 million free API tokens at [jina.ai](https://jina.ai) for embeddings and reranking
+
+### Why This Change:
+- **Native graph capabilities**: SurrealDB provides built-in graph database features
+- **Unified storage**: Single database for both vectors and graph relationships
+- **Cloud-native**: Better support for distributed deployments
+- **Reduced complexity**: Eliminates custom RocksDB integration layer
+
+**See [CHANGELOG.md](CHANGELOG.md) for detailed migration guide.**
 
 ---
 
@@ -179,7 +222,7 @@ ollama_url = "http://localhost:11434"
 - Install and launch the app
 
 **Step 2: Download models in LM Studio**
-- **Embedding model:** `jinaai/jina-code-embeddings-1.5b`
+- **Embedding model:** `jinaai/jina-embeddings-v4`
 - **LLM model (optional):** `lmstudio-community/DeepSeek-Coder-V2-Lite-Instruct-GGUF`
 
 **Step 3: Start LM Studio server**
@@ -200,9 +243,9 @@ Create `~/.codegraph/config.toml`:
 ```toml
 [embedding]
 provider = "lmstudio"
-model = "jinaai/jina-code-embeddings-1.5b"
+model = "jinaai/jina-embeddings-v4"
 lmstudio_url = "http://localhost:1234"
-dimension = 1536
+dimension = 2048
 
 [llm]
 enabled = true
@@ -260,9 +303,9 @@ The wizard will guide you through configuration.
 ```toml
 [embedding]
 provider = "jina" # or openai
-model = "jina-code-embeddings-1.5b"
+model = "jina-embeddings-v4"
 openai_api_key = "sk-..."  # or set OPENAI_API_KEY env var
-dimension = 1536
+dimension = 2048
 
 [llm]
 enabled = true
@@ -276,9 +319,9 @@ context_window = 200000
 ```toml
 [embedding]
 provider = "jina" # or openai
-model = "jina-code-embeddings-1.5b"
+model = "jina-embeddings-v4"
 openai_api_key = "sk-..."
-dimension = 1536
+dimension = 2048
 
 [llm]
 enabled = true
@@ -312,7 +355,7 @@ anthropic_api_key = "sk-ant-..."
 provider = "openai"  # or "jina"
 model = "text-embedding-3-small"
 openai_api_key = "sk-..."
-dimension = 1536
+dimension = 2048
 
 [llm]
 enabled = true
@@ -328,9 +371,9 @@ context_window = 2000000  # 2M tokens!
 ```toml
 [embedding]
 provider = "jina"  # or "openai"
-model = "jina-code-embeddings-1.5b"
+model = "jina-embeddings-v4"
 openai_api_key = "sk-..."
-dimension = 1536
+dimension = 2048
 
 [vector_store]
 backend = "surrealdb"  # Instead of "faiss"
@@ -411,8 +454,8 @@ Configuration is loaded from (in order):
 ```toml
 [embedding]
 provider = "lmstudio"  # or "onnx", "ollama", "openai"
-model = "jinaai/jina-code-embeddings-1.5b"
-dimension = 1536
+model = "jinaai/jina-embeddings-v4"
+dimension = 2048
 batch_size = 64
 
 [llm]