multiproject

Author: docxology

.cursorrules/AGENTS.md

@@ -38,17 +38,17 @@ This directory contains comprehensive development standards, coding guidelines,
 - Tests: `tests/infrastructure/`
 
 **Layer 2: Project** (Specific, customizable)
-- Location: `project/src/` (project-specific code)
+- Location: `projects/{name}/src/` (project-specific code)
 - Research-specific code
 - Uses infrastructure utilities
 - 90% minimum test coverage (currently 100% - perfect coverage!)
-- Tests: `project/tests/`
-- Scripts: `project/scripts/` (thin orchestrators)
+- Tests: `projects/{name}/tests/`
+- Scripts: `projects/{name}/scripts/` (thin orchestrators)
 
 ### 2. Thin Orchestrator Pattern
 
-- **Business logic** → `project/src/` or `infrastructure/`
-- **Orchestration** → `scripts/` (root, generic) or `project/scripts/` (project-specific)
+- **Business logic** → `projects/{name}/src/` or `infrastructure/`
+- **Orchestration** → `scripts/` (root, generic) or `projects/{name}/scripts/` (project-specific)
 - **No logic in scripts** - only coordination
 
 ### 3. Quality Standards
@@ -216,8 +216,8 @@ As shown in \eqref{eq:objective}, the objective function...
 
 **Related Documentation:**
 - [manuscript_style.md](manuscript_style.md) - Complete manuscript formatting guide
-- [../project/manuscript/AGENTS.md](../project/manuscript/AGENTS.md) - Manuscript documentation
-- [../docs/MARKDOWN_TEMPLATE_GUIDE.md](../docs/MARKDOWN_TEMPLATE_GUIDE.md) - Markdown guide
+- [../projects/project/manuscript/AGENTS.md](../projects/project/manuscript/AGENTS.md) - Manuscript documentation
+- [../docs/usage/MARKDOWN_TEMPLATE_GUIDE.md](../docs/usage/MARKDOWN_TEMPLATE_GUIDE.md) - Markdown guide
 
 ## Testing Standards
 
@@ -373,11 +373,12 @@ template/
 │   ├── llm/               # LLM integration
 │   ├── rendering/         # Multi-format rendering
 │   └── scientific/        # Scientific dev tools
-├── project/               # [LAYER 2] Research code
-│   ├── src/               # Project-specific algorithms
-│   ├── tests/             # Project tests
-│   ├── scripts/           # Project orchestrators
-│   └── manuscript/       # Research content
+├── projects/             # [LAYER 2] Research projects
+│   ├── {name}/           # [LAYER 2] Research code
+│   │   ├── src/           # Project-specific algorithms
+│   │   ├── tests/         # Project tests
+│   │   ├── scripts/       # Project orchestrators
+│   │   └── manuscript/   # Research content
 ├── scripts/               # [LAYER 1] Generic entry points
 ├── tests/                 # [LAYER 1] Infrastructure tests
 ├── docs/                  # Documentation
@@ -417,7 +418,7 @@ template/
 
 - [Root AGENTS.md](../AGENTS.md) - System overview
 - [Infrastructure AGENTS.md](../infrastructure/AGENTS.md) - Infrastructure layer
-- [Project AGENTS.md](../project/AGENTS.md) - Project layer
+- [Project AGENTS.md](../projects/project/AGENTS.md) - Project layer
 - [docs/](../docs/) - Comprehensive guides
 
 ### External Resources
@@ -457,28 +458,28 @@ The .cursorrules standards align with and support the main documentation:
 |---|---|---|
 | System Design | [AGENTS.md](AGENTS.md) | [Root AGENTS.md](../AGENTS.md) |
 | Documentation Structure | [folder_structure.md](folder_structure.md) | [Root AGENTS.md](../AGENTS.md) |
-| Architecture | [AGENTS.md](AGENTS.md) | [docs/ARCHITECTURE.md](../docs/ARCHITECTURE.md) |
+| Architecture | [AGENTS.md](AGENTS.md) | [docs/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) |
 | Infrastructure | [infrastructure_modules.md](infrastructure_modules.md) | [infrastructure/AGENTS.md](../infrastructure/AGENTS.md) |
-| Error Handling | [error_handling.md](error_handling.md) | [docs/TROUBLESHOOTING_GUIDE.md](../docs/TROUBLESHOOTING_GUIDE.md) |
-| Security | [security.md](security.md) | [docs/SECURITY.md](../docs/SECURITY.md) |
-| Logging | [python_logging.md](python_logging.md) | [docs/LOGGING_GUIDE.md](../docs/LOGGING_GUIDE.md) |
+| Error Handling | [error_handling.md](error_handling.md) | [docs/TROUBLESHOOTING_GUIDE.md](../docs/operational/TROUBLESHOOTING_GUIDE.md) |
+| Security | [security.md](security.md) | [docs/SECURITY.md](../docs/development/SECURITY.md) |
+| Logging | [python_logging.md](python_logging.md) | [docs/LOGGING_GUIDE.md](../docs/operational/LOGGING_GUIDE.md) |
 | Testing | [testing_standards.md](testing_standards.md) | [tests/AGENTS.md](../tests/AGENTS.md) |
-| Code Style | [code_style.md](code_style.md) | [docs/BEST_PRACTICES.md](../docs/BEST_PRACTICES.md) |
-| Git Workflow | [git_workflow.md](git_workflow.md) | [docs/VERSION_CONTROL.md](../docs/VERSION_CONTROL.md) |
-| API Design | [api_design.md](api_design.md) | [docs/ARCHITECTURE.md](../docs/ARCHITECTURE.md) |
-| Reporting | [reporting.md](reporting.md) | [docs/ADVANCED_MODULES_GUIDE.md](../docs/ADVANCED_MODULES_GUIDE.md) |
-| Documentation | [documentation_standards.md](documentation_standards.md) | [docs/WORKFLOW.md](../docs/WORKFLOW.md) |
-| Type Safety | [type_hints_standards.md](type_hints_standards.md) | [docs/ARCHITECTURE.md](../docs/ARCHITECTURE.md) |
+| Code Style | [code_style.md](code_style.md) | [docs/BEST_PRACTICES.md](../docs/best-practices/BEST_PRACTICES.md) |
+| Git Workflow | [git_workflow.md](git_workflow.md) | [docs/VERSION_CONTROL.md](../docs/best-practices/VERSION_CONTROL.md) |
+| API Design | [api_design.md](api_design.md) | [docs/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) |
+| Reporting | [reporting.md](reporting.md) | [docs/ADVANCED_MODULES_GUIDE.md](../docs/modules/ADVANCED_MODULES_GUIDE.md) |
+| Documentation | [documentation_standards.md](documentation_standards.md) | [docs/WORKFLOW.md](../docs/core/WORKFLOW.md) |
+| Type Safety | [type_hints_standards.md](type_hints_standards.md) | [docs/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) |
 | LLM Integration | [llm_standards.md](llm_standards.md) | [infrastructure/llm/AGENTS.md](../infrastructure/llm/AGENTS.md) |
-| Manuscript Writing | [manuscript_style.md](manuscript_style.md) | [project/manuscript/AGENTS.md](../project/manuscript/AGENTS.md) |
-| Refactoring | [refactoring.md](refactoring.md) | [docs/BEST_PRACTICES.md](../docs/BEST_PRACTICES.md) |
+| Manuscript Writing | [manuscript_style.md](manuscript_style.md) | [project/manuscript/AGENTS.md](../projects/project/manuscript/AGENTS.md) |
+| Refactoring | [refactoring.md](refactoring.md) | [docs/BEST_PRACTICES.md](../docs/best-practices/BEST_PRACTICES.md) |
 
 ## Cross-Reference Guide
 
 **For Architecture Decisions:**
 → Check [AGENTS.md](AGENTS.md) for decision criteria  
-→ Read [../docs/ARCHITECTURE.md](../docs/ARCHITECTURE.md) for full architectural overview  
-→ Consult [../docs/THIN_ORCHESTRATOR_SUMMARY.md](../docs/THIN_ORCHESTRATOR_SUMMARY.md) for pattern details
+→ Read [../docs/core/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) for full architectural overview  
+→ Consult [../docs/architecture/THIN_ORCHESTRATOR_SUMMARY.md](../docs/architecture/THIN_ORCHESTRATOR_SUMMARY.md) for pattern details
 
 **For Infrastructure Development:**
 → Check [infrastructure_modules.md](infrastructure_modules.md) for standards  
@@ -487,8 +488,8 @@ The .cursorrules standards align with and support the main documentation:
 
 **For Code Quality:**
 → Check [error_handling.md](error_handling.md) and [python_logging.md](python_logging.md)  
-→ Read [../docs/BEST_PRACTICES.md](../docs/BEST_PRACTICES.md) for comprehensive practices  
-→ See [../docs/ERROR_HANDLING_GUIDE.md](../docs/ERROR_HANDLING_GUIDE.md) for detailed patterns
+→ Read [../docs/best-practices/BEST_PRACTICES.md](../docs/best-practices/BEST_PRACTICES.md) for comprehensive practices  
+→ See [../docs/operational/ERROR_HANDLING_GUIDE.md](../docs/operational/ERROR_HANDLING_GUIDE.md) for detailed patterns
 
 ## Quick Navigation Guide
 
@@ -507,10 +508,10 @@ The .cursorrules standards align with and support the main documentation:
 | Writing tests | [testing_standards.md](testing_standards.md) | [error_handling.md](error_handling.md) for error testing |
 | Creating modules | [infrastructure_modules.md](infrastructure_modules.md) | All of the above standards |
 | Writing docs | [documentation_standards.md](documentation_standards.md) | Specific guide for your doc type |
-| Writing manuscripts | [manuscript_style.md](manuscript_style.md) | [project/manuscript/AGENTS.md](../project/manuscript/AGENTS.md) for manuscript structure |
+| Writing manuscripts | [manuscript_style.md](manuscript_style.md) | [project/manuscript/AGENTS.md](../projects/project/manuscript/AGENTS.md) for manuscript structure |
 | Adding type hints | [type_hints_standards.md](type_hints_standards.md) | [documentation_standards.md](documentation_standards.md) for docstrings |
 | Using LLM/Ollama | [llm_standards.md](llm_standards.md) | [infrastructure_modules.md](infrastructure_modules.md) for module patterns |
-| Generating reports | [reporting.md](reporting.md) | [docs/ADVANCED_MODULES_GUIDE.md](../docs/ADVANCED_MODULES_GUIDE.md) for module details |
+| Generating reports | [reporting.md](reporting.md) | [docs/ADVANCED_MODULES_GUIDE.md](../docs/modules/ADVANCED_MODULES_GUIDE.md) for module details |
 
 ### By File Size & Detail Level
 
@@ -564,11 +565,11 @@ When creating a new .cursorrules file:
 - [`README.md`](README.md) - Quick reference guide
 - [`../AGENTS.md`](../AGENTS.md) - Complete system documentation
 - [`../infrastructure/AGENTS.md`](../infrastructure/AGENTS.md) - Infrastructure layer documentation
-- [`../project/AGENTS.md`](../project/AGENTS.md) - Project layer documentation
+- [`../projects/project/AGENTS.md`](../projects/project/AGENTS.md) - Project layer documentation
 
 **Related Documentation:**
-- [`../docs/ARCHITECTURE.md`](../docs/ARCHITECTURE.md) - System architecture overview
-- [`../docs/WORKFLOW.md`](../docs/WORKFLOW.md) - Development workflow
+- [`../docs/core/ARCHITECTURE.md`](../docs/core/ARCHITECTURE.md) - System architecture overview
+- [`../docs/core/WORKFLOW.md`](../docs/core/WORKFLOW.md) - Development workflow
 - [`../tests/AGENTS.md`](../tests/AGENTS.md) - Testing philosophy and guide
 
 ---

.cursorrules/README.md

@@ -246,5 +246,5 @@ Before commit:
 - See [AGENTS.md](AGENTS.md) for comprehensive documentation and navigation guide
 - See [Quick Navigation Guide](AGENTS.md#quick-navigation-guide) for activity-based guidance
 - See [../docs/AGENTS.md](../docs/AGENTS.md) for main project documentation
-- See [../docs/HOW_TO_USE.md](../docs/HOW_TO_USE.md) for complete usage guide
-- See [../docs/SECURITY.md](../docs/SECURITY.md) for security policy
+- See [../docs/core/HOW_TO_USE.md](../docs/core/HOW_TO_USE.md) for complete usage guide
+- See [../docs/development/SECURITY.md](../docs/development/SECURITY.md) for security policy

.cursorrules/api_design.md

@@ -731,5 +731,5 @@ def new_function_name(parameter: str) -> str:
 - [error_handling.md](error_handling.md) - Exception handling in APIs
 - [testing_standards.md](testing_standards.md) - Testing API contracts
 - [infrastructure_modules.md](infrastructure_modules.md) - Module API design
-- [../docs/API_REFERENCE.md](../docs/API_REFERENCE.md) - Complete API documentation
-- [../docs/ARCHITECTURE.md](../docs/ARCHITECTURE.md) - API architecture design
+- [../docs/reference/API_REFERENCE.md](../docs/reference/API_REFERENCE.md) - Complete API documentation
+- [../docs/core/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) - API architecture design

.cursorrules/code_style.md

@@ -524,4 +524,4 @@ Add to GitHub Actions workflow:
 - [error_handling.md](error_handling.md) - Exception handling patterns
 - [python_logging.md](python_logging.md) - Logging standards
 - [infrastructure_modules.md](infrastructure_modules.md) - Module development standards
-- [../docs/BEST_PRACTICES.md](../docs/BEST_PRACTICES.md) - Code quality best practices
+- [../docs/best-practices/BEST_PRACTICES.md](../docs/best-practices/BEST_PRACTICES.md) - Code quality best practices

.cursorrules/documentation_standards.md

@@ -524,14 +524,14 @@ Before committing documentation:
 ### Good AGENTS.md References
 
 - [infrastructure/AGENTS.md](../infrastructure/AGENTS.md) - Complete module docs
-- [project/src/AGENTS.md](../project/src/AGENTS.md) - Project code docs
+- [project/src/AGENTS.md](../projects/project/src/AGENTS.md) - Project code docs
 - [tests/AGENTS.md](../tests/AGENTS.md) - Test framework docs
 
 ### Good README.md References
 
 - [infrastructure/README.md](../infrastructure/README.md) - Quick patterns
 - [scripts/README.md](../scripts/README.md) - Quick commands
-- [project/README.md](../project/README.md) - Project quick start
+- [project/README.md](../projects/project/README.md) - Project quick start
 
 ## See Also
 
@@ -540,7 +540,7 @@ Before committing documentation:
 - [../docs/DOCUMENTATION_INDEX.md](../docs/DOCUMENTATION_INDEX.md) - Complete documentation index
 - [../docs/AGENTS.md](../docs/AGENTS.md) - Main project documentation
 - [../AGENTS.md](../AGENTS.md) - Root documentation
-- [../docs/ARCHITECTURE.md](../docs/ARCHITECTURE.md) - System architecture
+- [../docs/core/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) - System architecture
 
 
 

.cursorrules/error_handling.md

@@ -357,7 +357,7 @@ def test_exception_chaining():
 
 ## See Also
 
-- [Error Handling Guide](../docs/ERROR_HANDLING_GUIDE.md) - Comprehensive error handling patterns
+- [Error Handling Guide](../docs/operational/ERROR_HANDLING_GUIDE.md) - Comprehensive error handling patterns
 - [Logging](python_logging.md) - Logging standards
 - [testing_standards.md](testing_standards.md) - Testing error conditions
 - [documentation_standards.md](documentation_standards.md) - Documenting exceptions

.cursorrules/git_workflow.md

@@ -469,5 +469,5 @@ git lfs track "*.pdf"
 - [testing_standards.md](testing_standards.md) - Testing patterns and coverage
 - [infrastructure_modules.md](infrastructure_modules.md) - Module development standards
 - [documentation_standards.md](documentation_standards.md) - Documentation writing guide
-- [../docs/VERSION_CONTROL.md](../docs/VERSION_CONTROL.md) - Version control best practices
-- [../docs/CI_CD_INTEGRATION.md](../docs/CI_CD_INTEGRATION.md) - CI/CD integration guide
+- [../docs/best-practices/VERSION_CONTROL.md](../docs/best-practices/VERSION_CONTROL.md) - Version control best practices
+- [../docs/operational/CI_CD_INTEGRATION.md](../docs/operational/CI_CD_INTEGRATION.md) - CI/CD integration guide

.cursorrules/infrastructure_modules.md

@@ -474,9 +474,9 @@ Before merging a new infrastructure module:
 ## References
 
 - [Infrastructure AGENTS.md](../infrastructure/AGENTS.md) - Module organization
-- [Advanced Modules Guide](../docs/ADVANCED_MODULES_GUIDE.md) - Complete guide to all advanced modules
-- [API Reference](../docs/API_REFERENCE.md) - Complete API documentation for all modules
-- [Two-Layer Architecture](../docs/TWO_LAYER_ARCHITECTURE.md) - Architecture explanation
+- [Advanced Modules Guide](../docs/modules/ADVANCED_MODULES_GUIDE.md) - Complete guide to all advanced modules
+- [API Reference](../docs/reference/API_REFERENCE.md) - Complete API documentation for all modules
+- [Two-Layer Architecture](../docs/architecture/TWO_LAYER_ARCHITECTURE.md) - Architecture explanation
 - [Testing Guide](testing_standards.md) - Testing infrastructure code
 - [Error Handling Guide](error_handling.md) - Exception patterns
 - [Logging Guide](python_logging.md) - Logging standards

.cursorrules/manuscript_style.md

@@ -1032,10 +1032,10 @@ the iterative algorithm described in Section \ref{sec:algorithm}.
 
 ## See Also
 
-- [project/manuscript/AGENTS.md](../project/manuscript/AGENTS.md) - Complete manuscript documentation
-- [project/manuscript/README.md](../project/manuscript/README.md) - Quick reference for manuscript
-- [docs/MARKDOWN_TEMPLATE_GUIDE.md](../docs/MARKDOWN_TEMPLATE_GUIDE.md) - Markdown and cross-referencing guide
-- [docs/MANUSCRIPT_NUMBERING_SYSTEM.md](../docs/MANUSCRIPT_NUMBERING_SYSTEM.md) - Section numbering system
+- [project/manuscript/AGENTS.md](../projects/project/manuscript/AGENTS.md) - Complete manuscript documentation
+- [project/manuscript/README.md](../projects/project/manuscript/README.md) - Quick reference for manuscript
+- [docs/MARKDOWN_TEMPLATE_GUIDE.md](../docs/usage/MARKDOWN_TEMPLATE_GUIDE.md) - Markdown and cross-referencing guide
+- [docs/MANUSCRIPT_NUMBERING_SYSTEM.md](../docs/usage/MANUSCRIPT_NUMBERING_SYSTEM.md) - Section numbering system
 - [code_style.md](code_style.md) - Code formatting standards
 - [documentation_standards.md](documentation_standards.md) - Documentation writing guide
 

.cursorrules/python_logging.md

@@ -382,7 +382,7 @@ def test_error_logging(caplog):
 
 ## See Also
 
-- [Logging Guide](../docs/LOGGING_GUIDE.md) - Comprehensive logging documentation
+- [Logging Guide](../docs/operational/LOGGING_GUIDE.md) - Comprehensive logging documentation
 - [Error Handling](error_handling.md) - Error handling patterns
 - [testing_standards.md](testing_standards.md) - Testing logging
 - [documentation_standards.md](documentation_standards.md) - Documenting logging