Refactor README, migrate detailed content to central docs

- Remove architecture mermaid diagram (moved to central docs)
- Remove admin utilities and data retention sections (migrated)
- Add links to central documentation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: vredchenko

README.md

@@ -1,23 +1,20 @@
-[![CI](https://github.com/DiamondLightSource/smartem-decisions/actions/workflows/ci.yml/badge.svg)](
-https://github.com/DiamondLightSource/smartem-decisions/actions/workflows/ci.yml)
-[![Coverage](https://codecov.io/gh/DiamondLightSource/smartem-decisions/branch/main/graph/badge.svg)](
-https://codecov.io/gh/DiamondLightSource/smartem-decisions)
+[![Built with Claude Code](https://img.shields.io/badge/Built%20with-Claude%20Code-6366f1?logo=claude)](https://claude.ai/code)
+[![CI](https://github.com/DiamondLightSource/smartem-decisions/actions/workflows/ci.yml/badge.svg)](https://github.com/DiamondLightSource/smartem-decisions/actions/workflows/ci.yml)
+[![Coverage](https://codecov.io/gh/DiamondLightSource/smartem-decisions/branch/main/graph/badge.svg)](https://codecov.io/gh/DiamondLightSource/smartem-decisions)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
 # SmartEM Decisions
 
-A comprehensive system for smart data collection and processing in cryo-electron microscopy, designed to optimize
-acquisition workflows through intelligent decision-making and real-time data analysis.
+A comprehensive system for smart data collection and processing in cryo-electron microscopy, designed to optimise acquisition workflows through intelligent decision-making and real-time data analysis.
 
 ## Quick Links
 
 Source          | <https://github.com/DiamondLightSource/smartem-decisions>
 :---:           | :---:
 Docker          | `docker run ghcr.io/DiamondLightSource/smartem-backend:latest`
-Documentation   | <https://DiamondLightSource.github.io/smartem-decisions>
+Documentation   | <https://DiamondLightSource.github.io/smartem-devtools>
 Releases        | <https://github.com/DiamondLightSource/smartem-decisions/releases>
 Project Board   | <https://github.com/orgs/DiamondLightSource/projects/33/views/1>
-Test Datasets   | <https://gitlab.diamond.ac.uk/scisoft/cryoem/smartem-decisions-test-datasets>
 
 ## System Components
 
@@ -28,203 +25,31 @@ Test Datasets   | <https://gitlab.diamond.ac.uk/scisoft/cryoem/smartem-decisions
 
 ## Quick Start
 
-```python
-from smartem_backend._version import __version__
-
-print(f"Hello smartem_backend {__version__}")
-```
-
-## Architecture Overview
-
-```mermaid
-flowchart TD
-    %% Equipment and Data Collection Layer
-    subgraph facility["Diamond Light Source Facility"]
-        microscope["Cryo-EM Microscope"]
-        athena_hw["Athena Hardware"]
-        epu["EPU Software<br/>(ThermoFisher)"]
-        gpfs[("GPFS Storage")]
-    end
-
-    %% Agent Layer
-    subgraph agent["smartem_agent (Windows)"]
-        fs_watcher["File System Watcher"]
-        fs_parser["EPU Data Parser"]
-        sse_client["SSE Client"]
-    end
-
-    %% Backend Services Layer
-    subgraph backend["smartem_backend (Kubernetes)"]
-        api_server["FastAPI Server<br/>SSE + HTTP API"]
-        consumer["RabbitMQ Consumer"]
-        conn_mgr["Connection Manager"]
-    end
-
-    %% Infrastructure Layer
-    subgraph infra["Infrastructure (Kubernetes)"]
-        db[("PostgreSQL<br/>Sessions & Instructions")]
-        mq[("RabbitMQ<br/>Event Streaming")]
-        log["Logging<br/>(Graylog)"]
-    end
-
-    %% Additional Packages
-    common["smartem_common<br/>(Shared Schemas)"]
-    athena_api["athena_api<br/>(API Client)"]
-
-    %% Data Flow Connections
-    microscope --> epu
-    athena_hw --> microscope
-    epu --> gpfs
-    gpfs --> fs_watcher
-    fs_watcher --> fs_parser
-    fs_parser --> sse_client
-
-    %% External Processing → RabbitMQ → Backend
-    subgraph external["External Processing Systems"]
-        ml_pipeline["ML Pipeline<br/>(Quality Predictions)"]
-        image_proc["Image Processing<br/>(Motion/CTF/Particles)"]
-    end
-
-    ml_pipeline -.->|"Model Predictions<br/>Parameter Updates"| mq
-    image_proc -.->|"Processing Results<br/>Quality Metrics"| mq
-
-    %% Backend Communication
-    sse_client <-.->|"SSE Streams &<br/>HTTP ACKs"| api_server
-
-    %% Backend Internal
-    api_server --> db
-    api_server --> mq
-    api_server --> log
-    consumer --> db
-    consumer --> mq
-    conn_mgr --> db
-
-    %% External Integration
-    api_server --> athena_api
-    athena_api -.->|"Control Commands<br/>(reorder, skip)"| athena_hw
-
-    %% Package Dependencies
-    backend -.-> common
-    agent -.-> common
-
-    %% Styling
-    classDef facility fill:#e8f5e8,stroke:#28a745,stroke-width:2px
-    classDef agent fill:#fff5e6,stroke:#e67e22,stroke-width:2px
-    classDef backend fill:#e6f3ff,stroke:#0066cc,stroke-width:2px
-    classDef infra fill:#f5f5f5,stroke:#666,stroke-width:2px
-    classDef packages fill:#f9f9f9,stroke:#999,stroke-width:1px
-    classDef external fill:#f8f9fa,stroke:#6c757d,stroke-width:2px
-
-    class facility facility
-    class agent agent
-    class backend backend
-    class infra infra
-    class common,athena_api packages
-    class external,ml_pipeline,image_proc external
-```
-
-## Development Setup
-
 ```bash
-# venv and requirements
+# Create virtual environment and install
 python -m venv .venv
 source .venv/bin/activate
-pip install -e .[dev] # or .[backend] for production
+pip install -e .[dev]
 
-# Start services with verbosity controls:
-python -m smartem_backend.api_server               # HTTP API server
-python -m smartem_backend.consumer -v              # Message queue consumer with INFO logging
-python -m smartem_agent watch /path/to/data -v     # File watcher with INFO logging
-
-# For testing file watcher with simulated EPU data:
-python tools/fsrecorder/fsrecorder.py replay recording.tar.gz /path/to/data --fast
-
-# For testing external message processing:
-python tools/external_message_simulator.py list-messages           # See available message types
-python tools/external_message_simulator.py workflow-simulation --gridsquare-id "DEV_001"
-
-# For testing agent-backend communication:
-python tools/sse_client_example.py                                 # Test SSE instruction delivery
+# Start services
+python -m smartem_backend.api_server      # HTTP API server
+python -m smartem_backend.consumer -v     # Message queue consumer
 ```
 
-## Administrative Utilities
-
-After installation with `pip install -e .[all]`, the following command-line utilities are available for system administration and maintenance:
-
-### Agent Communication Management
-
-- **`smartem.agent-cleanup`** - Data lifecycle and cleanup operations for agent communication data
-  ```bash
-  # Check current database usage and statistics
-  smartem.agent-cleanup --operation=stats
-  
-  # Run full cleanup with scientific retention policy (7-year audit trail)
-  smartem.agent-cleanup --operation=cleanup --policy=scientific
-  
-  # Run cleanup with development retention policy (shorter retention)
-  smartem.agent-cleanup --operation=cleanup --policy=development
-  
-  # Clean only stale connections
-  smartem.agent-cleanup --operation=connections
-  
-  # Preview what would be cleaned without making changes
-  smartem.agent-cleanup --operation=cleanup --dry-run
-  ```
-
-### ML Model and Prediction Management
-
-- **`smartem.register-prediction-model`** - Register new machine learning prediction models
-  ```bash
-  smartem.register-prediction-model "ResNet-50" "Deep learning model for cryo-EM image quality assessment"
-  ```
-
-- **`smartem.init-model-weight`** - Initialize model weights for specific grids
-  ```bash
-  smartem.init-model-weight --help  # View available options
-  ```
-
-- **`smartem.random-model-predictions`** - Generate test predictions for development and testing
-  ```bash
-  smartem.random-model-predictions --help  # View available options
-  ```
-
-- **`smartem.random-prior-updates`** - Simulate prior updates for testing workflows
-  ```bash
-  smartem.random-prior-updates --help  # View available options
-  ```
-
-### Development and Integration Tools
-
-- **`smartem_agent_tools`** - Agent development and debugging utilities
-
-### Data Retention Policies
-
-The `smartem.agent-cleanup` utility supports two built-in retention policies:
-
-- **Scientific Compliance** (default): Conservative retention suitable for scientific research
-  - Connections: 48 hours
-  - Instructions: 365 days  
-  - Completed sessions: 2 years
-  - Acknowledgements: 7 years (regulatory compliance)
+## Documentation
 
-- **Development**: Shorter retention for development environments
-  - Connections: 4 hours
-  - Instructions: 7 days
-  - Completed sessions: 14 days
-  - Acknowledgements: 30 days
+Full documentation: <https://DiamondLightSource.github.io/smartem-devtools>
 
-All utilities include comprehensive `--help` documentation for detailed usage instructions.
+- [Backend API Server](https://diamondlightsource.github.io/smartem-devtools/backend/api-server)
+- [Agent Deployment](https://diamondlightsource.github.io/smartem-devtools/agent/deployment)
+- [Admin Utilities](https://diamondlightsource.github.io/smartem-devtools/backend/admin-utilities)
+- [Data Retention Policies](https://diamondlightsource.github.io/smartem-devtools/operations/data-retention)
+- [Kubernetes Deployment](https://diamondlightsource.github.io/smartem-devtools/operations/kubernetes)
 
-## More Information
+## Contributing
 
-For detailed documentation including:
+See the [contribution guide](https://diamondlightsource.github.io/smartem-devtools/development/contributing) for development workflow and code standards.
 
-- [Logging Configuration](docs/how-to/configure-logging.md)
-- [Running Backend Services](docs/how-to/run-backend.md)
-- [Running Agent Services](docs/how-to/run-agent.md)
-- [EPU Data Structure Explanations](docs/explanations/epu-data-structures.md)
-- [Kubernetes Deployment](docs/how-to/deploy-kubernetes.md)
-- [Development Tools](docs/how-to/development-tools.md)
-- And more...
+## Licence
 
-See https://DiamondLightSource.github.io/smartem-decisions for complete documentation.
+Apache-2.0