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Add GLM click analysis notebooks and supporting files
- Update glm_clicks_to_dv_glmnet.ipynb with improved GLM implementation - Add glm_click_spacing_analysis_v001.ipynb for temporal click pattern analysis - Add glm_clicks_recovery_demo_v001.ipynb for kernel recovery demonstration - Add sklearn_vs_glmnet_comparison.md documenting differences between implementations - Add plan_mode_violation_log.md for tracking analysis issues - Add .spec-workflow/ templates for project documentation structure - Update CLAUDE.md with enhanced project preferences and instructions These changes improve the GLM analysis pipeline for linking Poisson click inputs to decision variables in the rat behavioral data.
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‎.spec-workflow/config.example.toml‎

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# Spec Workflow MCP Server Configuration File
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# ============================================
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#
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# This is an example configuration file for the Spec Workflow MCP Server.
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# Copy this file to 'config.toml' in the same directory to use it.
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#
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# Configuration Precedence:
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# 1. Command-line arguments (highest priority)
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# 2. Config file settings
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# 3. Built-in defaults (lowest priority)
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#
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# All settings are optional. Uncomment and modify as needed.
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# Please note that not all MCP clients will support loading this config file due to the nature of where they are running from.
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# Project directory path
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# The root directory of your project where spec files are located.
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# Note: You may have to use double slashes (\\) instead of single slashes (/) on Windows or for certain clients.
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# Supports tilde (~) expansion for home directory.
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# Default: current working directory
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# projectDir = "."
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# projectDir = "~/my-project"
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# projectDir = "/absolute/path/to/project"
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# Dashboard port
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# The port number for the web dashboard.
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# Must be between 1024 and 65535.
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# Default: ephemeral port (automatically assigned)
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# port = 3000
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# Auto-start dashboard
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# Automatically launch the dashboard when the MCP server starts.
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# The dashboard will open in your default browser.
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# Default: false
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# autoStartDashboard = false
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# Dashboard-only mode
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# Run only the web dashboard without the MCP server.
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# Useful for standalone dashboard usage.
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# Default: false
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# dashboardOnly = false
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# Language
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# Set the interface language for internationalization (i18n).
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# Available languages depend on your installation.
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# Common values: "en" (English), "ja" (Japanese), etc.
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# Default: system language or "en"
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# lang = "en"
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# Example configurations:
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# =====================
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# Example 1: Development setup with auto-started dashboard
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# ----------------------------------------------------------
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# projectDir = "~/dev/my-project"
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# autoStartDashboard = true
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# port = 3456
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# Example 2: Production MCP server without dashboard
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# ---------------------------------------------------
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# projectDir = "/var/projects/production"
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# autoStartDashboard = false
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# Example 3: Dashboard-only mode for viewing specs
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# -------------------------------------------------
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# projectDir = "."
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# dashboardOnly = true
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# port = 8080
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# Example 4: Japanese language interface
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# ---------------------------------------
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# lang = "ja"
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# autoStartDashboard = true

‎.spec-workflow/templates/design-template.md‎

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# Design Document
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## Overview
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[High-level description of the feature and its place in the overall system]
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## Steering Document Alignment
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### Technical Standards (tech.md)
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[How the design follows documented technical patterns and standards]
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### Project Structure (structure.md)
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[How the implementation will follow project organization conventions]
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## Code Reuse Analysis
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[What existing code will be leveraged, extended, or integrated with this feature]
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### Existing Components to Leverage
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- **[Component/Utility Name]**: [How it will be used]
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- **[Service/Helper Name]**: [How it will be extended]
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### Integration Points
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- **[Existing System/API]**: [How the new feature will integrate]
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- **[Database/Storage]**: [How data will connect to existing schemas]
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## Architecture
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[Describe the overall architecture and design patterns used]
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### Modular Design Principles
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- **Single File Responsibility**: Each file should handle one specific concern or domain
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- **Component Isolation**: Create small, focused components rather than large monolithic files
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- **Service Layer Separation**: Separate data access, business logic, and presentation layers
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- **Utility Modularity**: Break utilities into focused, single-purpose modules
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```mermaid
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graph TD
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A[Component A] --> B[Component B]
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B --> C[Component C]
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```
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## Components and Interfaces
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### Component 1
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- **Purpose:** [What this component does]
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- **Interfaces:** [Public methods/APIs]
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- **Dependencies:** [What it depends on]
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- **Reuses:** [Existing components/utilities it builds upon]
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### Component 2
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- **Purpose:** [What this component does]
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- **Interfaces:** [Public methods/APIs]
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- **Dependencies:** [What it depends on]
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- **Reuses:** [Existing components/utilities it builds upon]
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## Data Models
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### Model 1
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```
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[Define the structure of Model1 in your language]
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- id: [unique identifier type]
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- name: [string/text type]
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- [Additional properties as needed]
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```
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### Model 2
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```
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[Define the structure of Model2 in your language]
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- id: [unique identifier type]
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- [Additional properties as needed]
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```
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## Error Handling
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### Error Scenarios
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1. **Scenario 1:** [Description]
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- **Handling:** [How to handle]
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- **User Impact:** [What user sees]
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2. **Scenario 2:** [Description]
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- **Handling:** [How to handle]
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- **User Impact:** [What user sees]
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## Testing Strategy
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### Unit Testing
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- [Unit testing approach]
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- [Key components to test]
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### Integration Testing
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- [Integration testing approach]
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- [Key flows to test]
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### End-to-End Testing
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- [E2E testing approach]
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- [User scenarios to test]

‎.spec-workflow/templates/product-template.md‎

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# Product Overview
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## Product Purpose
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[Describe the core purpose of this product/project. What problem does it solve?]
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## Target Users
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[Who are the primary users of this product? What are their needs and pain points?]
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## Key Features
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[List the main features that deliver value to users]
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1. **Feature 1**: [Description]
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2. **Feature 2**: [Description]
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3. **Feature 3**: [Description]
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## Business Objectives
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[What are the business goals this product aims to achieve?]
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- [Objective 1]
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- [Objective 2]
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- [Objective 3]
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## Success Metrics
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[How will we measure the success of this product?]
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- [Metric 1]: [Target]
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- [Metric 2]: [Target]
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- [Metric 3]: [Target]
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## Product Principles
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[Core principles that guide product decisions]
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1. **[Principle 1]**: [Explanation]
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2. **[Principle 2]**: [Explanation]
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3. **[Principle 3]**: [Explanation]
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## Monitoring & Visibility (if applicable)
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[How do users track progress and monitor the system?]
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- **Dashboard Type**: [e.g., Web-based, CLI, Desktop app]
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- **Real-time Updates**: [e.g., WebSocket, polling, push notifications]
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- **Key Metrics Displayed**: [What information is most important to surface]
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- **Sharing Capabilities**: [e.g., read-only links, exports, reports]
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## Future Vision
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[Where do we see this product evolving in the future?]
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### Potential Enhancements
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- **Remote Access**: [e.g., Tunnel features for sharing dashboards with stakeholders]
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- **Analytics**: [e.g., Historical trends, performance metrics]
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- **Collaboration**: [e.g., Multi-user support, commenting]

‎.spec-workflow/templates/requirements-template.md‎

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# Requirements Document
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## Introduction
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[Provide a brief overview of the feature, its purpose, and its value to users]
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## Alignment with Product Vision
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[Explain how this feature supports the goals outlined in product.md]
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## Requirements
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### Requirement 1
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**User Story:** As a [role], I want [feature], so that [benefit]
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#### Acceptance Criteria
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1. WHEN [event] THEN [system] SHALL [response]
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2. IF [precondition] THEN [system] SHALL [response]
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3. WHEN [event] AND [condition] THEN [system] SHALL [response]
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### Requirement 2
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**User Story:** As a [role], I want [feature], so that [benefit]
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#### Acceptance Criteria
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1. WHEN [event] THEN [system] SHALL [response]
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2. IF [precondition] THEN [system] SHALL [response]
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## Non-Functional Requirements
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### Code Architecture and Modularity
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- **Single Responsibility Principle**: Each file should have a single, well-defined purpose
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- **Modular Design**: Components, utilities, and services should be isolated and reusable
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- **Dependency Management**: Minimize interdependencies between modules
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- **Clear Interfaces**: Define clean contracts between components and layers
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### Performance
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- [Performance requirements]
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### Security
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- [Security requirements]
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### Reliability
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- [Reliability requirements]
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### Usability
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- [Usability requirements]

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