Update and organize documentation

- Renamed all uppercase markdown files to lowercase for consistency
  - ARCHITECTURE.md -> architecture.md
  - DEVELOPER_GUIDE.md -> developer-guide.md
  - TIMESTAMP_EVENTS_GUIDE.md -> timestamp-events-guide.md
  - SERIALIZATION_NOTES.txt -> serialization-notes.txt

- Removed all Raft references from documentation
  - Updated build-fixes-summary.md
  - Updated testing-guide.md
  - Updated test-infrastructure.md
  - Updated simulation-builder-framework.md

- Created index.md for easy documentation navigation
  - Organized docs by category (Architecture, Testing, GUI Decoupling, etc.)
  - Added quick links for different user types
  - Included documentation standards and contribution guidelines

All documentation is now consistent and up-to-date with the current codebase.

🤖 Generated with Claude Code
https://claude.ai/code

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

1 files changed, 0 insertions, 397 deletions

diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
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-# DS-Sim Architecture Documentation
-
-## Table of Contents
-1. [Overview](#overview)
-2. [Core Architecture](#core-architecture)
-3. [Event-Driven Design](#event-driven-design)
-4. [Protocol Framework](#protocol-framework)
-5. [Time Management](#time-management)
-6. [Message System](#message-system)
-7. [Component Diagrams](#component-diagrams)
-8. [Sequence Diagrams](#sequence-diagrams)
-
-## Overview
-
-DS-Sim is an event-driven distributed systems simulator built with Java. It provides a visual environment for simulating and understanding distributed algorithms, protocols, and time synchronization mechanisms.
-
-### Key Design Principles
-- **Event-Driven Architecture**: All actions are modeled as events
-- **Pluggable Protocols**: Easy to add new distributed algorithms
-- **Visual Feedback**: Real-time visualization of process states and messages
-- **Time Simulation**: Support for logical clocks and clock drift
-
-## Core Architecture
-
-### Layer Diagram
-```
-┌─────────────────────────────────────────────────────────────┐
-│                    User Interface Layer                      │
-│  VSSimulatorFrame, VSSimulator, VSSimulatorVisualization   │
-├─────────────────────────────────────────────────────────────┤
-│                    Protocol Layer                            │
-│  VSAbstractProtocol, Protocol Implementations               │
-├─────────────────────────────────────────────────────────────┤
-│                    Event System Layer                        │
-│  VSAbstractEvent, VSTask, VSTaskManager                     │
-├─────────────────────────────────────────────────────────────┤
-│                    Core Process Layer                        │
-│  VSAbstractProcess, VSInternalProcess, VSMessage            │
-├─────────────────────────────────────────────────────────────┤
-│                    Infrastructure Layer                      │
-│  Time Management, Serialization, Utilities                  │
-└─────────────────────────────────────────────────────────────┘
-```
-
-### Component Overview
-
-```mermaid
-graph TB
-    subgraph UI[User Interface]
-        Frame[VSSimulatorFrame]
-        Sim[VSSimulator]
-        Viz[VSSimulatorVisualization]
-    end
-    
-    subgraph Core[Core Components]
-        TM[VSTaskManager]
-        IP[VSInternalProcess]
-        Msg[VSMessage]
-    end
-    
-    subgraph Events[Event System]
-        AE[VSAbstractEvent]
-        Task[VSTask]
-        RE[VSRegisteredEvents]
-    end
-    
-    subgraph Protocols[Protocols]
-        AP[VSAbstractProtocol]
-        PP[PingPongProtocol]
-        BC[BroadcastProtocol]
-        TC[TwoPhaseCommit]
-    end
-    
-    Frame --> Sim
-    Sim --> Viz
-    Viz --> TM
-    TM --> Task
-    Task --> AE
-    IP --> Msg
-    AP --> AE
-    PP --> AP
-    BC --> AP
-    TC --> AP
-```
-
-## Event-Driven Design
-
-The simulator operates on an event-driven model where all actions are encapsulated as events that are scheduled and executed by the task manager.
-
-### Event Hierarchy
-
-```mermaid
-classDiagram
-    class VSAbstractEvent {
-        <<abstract>>
-        +onInit()
-        +onStart()
-        +getClassname()
-        +isInternalEvent()
-        +shouldIncreaseTimestamps()
-    }
-    
-    class VSAbstractProtocol {
-        <<abstract>>
-        +onServerInit()
-        +onClientInit()
-        +onServerRecv()
-        +onClientRecv()
-        +sendMessage()
-    }
-    
-    class VSProcessCrashEvent {
-        +onStart()
-    }
-    
-    class VSMessageReceiveEvent {
-        +onStart()
-    }
-    
-    class VSTimestampTriggeredEvent {
-        <<abstract>>
-        +checkCondition()
-        +onTimestampReached()
-    }
-    
-    VSAbstractEvent <|-- VSAbstractProtocol
-    VSAbstractEvent <|-- VSProcessCrashEvent
-    VSAbstractEvent <|-- VSMessageReceiveEvent
-    VSAbstractEvent <|-- VSTimestampTriggeredEvent
-```
-
-### Event Lifecycle
-
-1. **Creation**: Events are created with specific parameters
-2. **Initialization**: `onInit()` is called once when first added
-3. **Scheduling**: Events are wrapped in `VSTask` with execution time
-4. **Execution**: `onStart()` is called when scheduled time arrives
-5. **Completion**: Event completes or schedules new events
-
-## Protocol Framework
-
-Protocols implement distributed algorithms and define client-server communication patterns.
-
-### Protocol Structure
-
-```mermaid
-stateDiagram-v2
-    [*] --> Uninitialized
-    Uninitialized --> ServerInit: isServer
-    Uninitialized --> ClientInit: isClient
-    
-    ServerInit --> ServerReady
-    ClientInit --> ClientReady
-    
-    ServerReady --> ServerStart: hasOnServerStart
-    ClientReady --> ClientStart: !hasOnServerStart
-    
-    ServerReady --> ServerRecv: receive message
-    ClientReady --> ClientRecv: receive message
-    
-    ServerReady --> ServerSchedule: scheduled event
-    ClientReady --> ClientSchedule: scheduled event
-```
-
-### Protocol Implementation Pattern
-
-```java
-public class MyProtocol extends VSAbstractProtocol {
-    public MyProtocol() {
-        super(HAS_ON_SERVER_START); // or HAS_ON_CLIENT_START
-    }
-    
-    // Server-side methods
-    public void onServerInit() { /* Initialize server state */ }
-    public void onServerStart() { /* Server begins protocol */ }
-    public void onServerRecv(VSMessage msg) { /* Handle client message */ }
-    public void onServerSchedule() { /* Periodic server action */ }
-    
-    // Client-side methods  
-    public void onClientInit() { /* Initialize client state */ }
-    public void onClientStart() { /* Client begins protocol */ }
-    public void onClientRecv(VSMessage msg) { /* Handle server message */ }
-    public void onClientSchedule() { /* Periodic client action */ }
-}
-```
-
-## Time Management
-
-The simulator supports multiple time representations for distributed systems research.
-
-### Time Types
-
-```mermaid
-graph LR
-    subgraph Time System
-        GT[Global Time<br/>Simulation Clock]
-        LT[Local Time<br/>Process Clock]
-        LAM[Lamport Time<br/>Logical Clock]
-        VT[Vector Time<br/>Vector Clock]
-    end
-    
-    GT --> LT
-    LT --> LAM
-    LT --> VT
-```
-
-### Clock Synchronization
-
-- **Global Time**: Absolute simulation time (milliseconds)
-- **Local Time**: Process time with configurable drift
-- **Lamport Time**: Increments on events and messages
-- **Vector Time**: Array of logical times for each process
-
-### Clock Drift Simulation
-
-```
-Local Time = Global Time + Accumulated Drift
-Drift Rate = Clock Variance (e.g., -0.1 to +0.1)
-```
-
-## Message System
-
-Messages in DS-Sim carry protocol data between processes with automatic timestamp management.
-
-### Message Flow
-
-```mermaid
-sequenceDiagram
-    participant P1 as Process 1
-    participant TM as TaskManager
-    participant Net as Network Sim
-    participant P2 as Process 2
-    
-    P1->>P1: Increase timestamps
-    P1->>TM: Create send task
-    TM->>Net: Schedule with delay
-    Net->>TM: Create receive task
-    TM->>P2: Deliver message
-    P2->>P2: Update timestamps
-    P2->>P2: Process message
-```
-
-### Message Properties
-
-- **Sender/Receiver**: Process IDs
-- **Protocol**: Associated protocol class
-- **Timestamps**: Lamport and vector times
-- **Payload**: Serializable data
-- **Type**: Server or client message
-
-## Component Diagrams
-
-### Task Management System
-
-```mermaid
-graph TB
-    subgraph TaskManager
-        PQ[Priority Queue<br/>Time-ordered tasks]
-        GL[Global Tasks<br/>Simulation time]
-        LL[Local Tasks<br/>Process time]
-    end
-    
-    subgraph Task Execution
-        Run[runTasks<br/>Main loop]
-        Exec[Execute task]
-        Update[Update times]
-    end
-    
-    PQ --> Run
-    Run --> Exec
-    Exec --> Update
-    Update --> PQ
-```
-
-### Process Architecture
-
-```mermaid
-classDiagram
-    class VSAbstractProcess {
-        <<abstract>>
-        #localTime: long
-        #globalTime: long
-        #lamportTime: long
-        #vectorTime: VSVectorTime
-        +increaseTime()
-        +sendMessage()
-    }
-    
-    class VSInternalProcess {
-        -clockVariance: float
-        -clockOffset: double
-        -vectorClockMonitor: VSVectorClockMonitor
-        +syncTime(globalTime)
-        +highlightOn()
-        +crash()
-        +recover()
-    }
-    
-    VSAbstractProcess <|-- VSInternalProcess
-```
-
-## Sequence Diagrams
-
-### Protocol Initialization
-
-```mermaid
-sequenceDiagram
-    participant UI as User Interface
-    participant Reg as VSRegisteredEvents
-    participant Proto as Protocol
-    participant Proc as Process
-    
-    UI->>Reg: Select protocol
-    Reg->>Proto: Create instance
-    Proto->>Proc: Set process
-    Proc->>Proto: isServer(true/false)
-    Proto->>Proto: onServerInit/onClientInit
-    Proto->>UI: Ready
-```
-
-### Event Processing Loop
-
-```mermaid
-sequenceDiagram
-    participant Viz as Visualization
-    participant TM as TaskManager
-    participant Task as VSTask
-    participant Event as Event
-    participant Proc as Process
-    
-    loop Simulation Loop
-        Viz->>TM: runTasks(currentTime)
-        TM->>TM: Get ready tasks
-        TM->>Task: run()
-        Task->>Event: onStart()
-        Event->>Proc: Update state
-        Event->>TM: Schedule new tasks
-    end
-```
-
-### Two-Phase Commit Example
-
-```mermaid
-sequenceDiagram
-    participant Coord as Coordinator
-    participant P1 as Process 1
-    participant P2 as Process 2
-    
-    Coord->>P1: VOTE_REQUEST
-    Coord->>P2: VOTE_REQUEST
-    P1->>Coord: VOTE_YES
-    P2->>Coord: VOTE_YES
-    Coord->>Coord: All votes YES
-    Coord->>P1: GLOBAL_COMMIT
-    Coord->>P2: GLOBAL_COMMIT
-    P1->>Coord: ACK
-    P2->>Coord: ACK
-```
-
-## Adding New Components
-
-### Creating a New Event
-
-1. Extend `VSAbstractEvent`
-2. Implement `onInit()` and `onStart()`
-3. Register in `VSRegisteredEvents.init()`
-
-### Creating a New Protocol
-
-1. Extend `VSAbstractProtocol`
-2. Implement required abstract methods
-3. Choose `HAS_ON_SERVER_START` or `HAS_ON_CLIENT_START`
-4. Register in `VSRegisteredEvents.init()`
-
-### Creating Timestamp-Triggered Events
-
-1. Extend `VSTimestampTriggeredEvent`
-2. Implement `onTimestampReached()`
-3. Configure trigger conditions
-4. Register with process monitor
-
-## Design Patterns Used
-
-- **Template Method**: Protocol base class defines structure
-- **Observer**: Event system for loose coupling
-- **Strategy**: Pluggable protocols and events
-- **Factory**: Event creation through registry
-- **Singleton**: Global registries and managers
-- **Command**: Events encapsulate actions
-
-## Future Architecture Improvements
-
-1. **GUI Separation**: Extract UI from business logic
-2. **Dependency Injection**: Remove static registries
-3. **Event Bus**: Decouple component communication
-4. **Plugin System**: Dynamic protocol loading
-5. **Reactive Streams**: Modern async event handling
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