update

Author: docxology

.coverage.project

@@ -5,10 +5,12 @@ Development standards and coding guidelines for the Research Project Template.
 ## Files
 
 ### Main Documents
+
 - **AGENTS.md** - overview and navigation (start here)
 - **README.md** - This file (quick reference)
 
 ### Development Standards
+
 - **error_handling.md** - Exception handling patterns
 - **python_logging.md** - Logging standards and best practices
 - **infrastructure_modules.md** - Infrastructure module development guide
@@ -22,7 +24,7 @@ Development standards and coding guidelines for the Research Project Template.
 - **api_design.md** - API design and interface standards
 - **manuscript_style.md** - Manuscript formatting and style standards
 - **reporting.md** - Reporting module standards and outputs
-- **refactoring.md** - **NEW**: Refactoring and modularization standards (clean break approach)
+- **refactoring.md** - Refactoring and modularization standards (clean break approach)
 
 ## Key Principles
 
@@ -226,9 +228,12 @@ Before commit:
 - [ ] All tests pass
 - [ ] No linter errors
 - [ ] Docs updated
-- [ ] Type hints ## Navigation Tips
+- [ ] Type hints on all public APIs
+
+## Navigation Tips
 
 **Pick your task:**
+
 - Writing code → [type_hints_standards.md](type_hints_standards.md)
 - Handling errors → [error_handling.md](error_handling.md)
 - Writing secure code → [security.md](security.md)
@@ -244,5 +249,5 @@ Before commit:
 - See [AGENTS.md](AGENTS.md) for 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/core/HOW_TO_USE.md](../docs/core/HOW_TO_USE.md) for usage guide
-- See [../docs/development/SECURITY.md](../docs/development/SECURITY.md) for security policy
+- See [../docs/core/how-to-use.md](../docs/core/how-to-use.md) for usage guide
+- See [../docs/development/security.md](../docs/development/security.md) for security policy

.cursorrules/AGENTS.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/reference/API_REFERENCE.md](../docs/reference/API_REFERENCE.md) - API documentation
-- [../docs/core/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) - API architecture design
+- [../docs/reference/api-reference.md](../docs/reference/api-reference.md) - API documentation
+- [../docs/core/architecture.md](../docs/core/architecture.md) - API architecture design

.cursorrules/README.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/BEST_PRACTICES.md](../docs/best-practices/BEST_PRACTICES.md) - Code quality best practices
+- [../docs/best-practices/best-practices.md](../docs/best-practices/best-practices.md) - Code quality best practices

.cursorrules/api_design.md

@@ -407,7 +407,7 @@ See [../AGENTS.md](../AGENTS.md) for overview
 
 - [Related Module](../infrastructure/AGENTS.md) - Infrastructure documentation
 - [External Resource](https://example.com) - External documentation
-- [Configuration Guide](CONFIGURATION.md) - Configuration documentation
+- [Configuration Guide](configuration.md) - Configuration documentation
 ```
 
 ## Format Standards
@@ -537,13 +537,7 @@ Before committing documentation:
 
 - [testing_standards.md](testing_standards.md) - Document tests properly
 - [type_hints_standards.md](type_hints_standards.md) - Type hint documentation
-- [../docs/DOCUMENTATION_INDEX.md](../docs/DOCUMENTATION_INDEX.md) - documentation index
+- [../docs/documentation-index.md](../docs/documentation-index.md) - documentation index
 - [../docs/AGENTS.md](../docs/AGENTS.md) - Main project documentation
 - [../AGENTS.md](../AGENTS.md) - Root documentation
-- [../docs/core/ARCHITECTURE.md](../docs/core/ARCHITECTURE.md) - System architecture
-
-
-
-
-
-
+- [../docs/core/architecture.md](../docs/core/architecture.md) - System architecture

.cursorrules/code_style.md

@@ -357,10 +357,7 @@ def test_exception_chaining():
 
 ## See Also
 
-- [Error Handling Guide](../docs/operational/ERROR_HANDLING_GUIDE.md) - error handling patterns
+- [Error Handling Guide](../docs/operational/error-handling-guide.md) - 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/documentation_standards.md

@@ -166,7 +166,7 @@ Additional documentation files should only be added when:
 | File | Purpose | When to Use |
 |------|---------|-------------|
 | `CHANGELOG.md` | Version history, migration notes | Versioned infrastructure modules |
-| `EXAMPLES.md` | Extended usage examples | Complex modules with many use cases |
+| `examples.md` | Extended usage examples | Complex modules with many use cases |
 | `TROUBLESHOOTING.md` | Detailed troubleshooting | Error-prone modules (LLM, rendering) |
 | `API.md` | API reference | Large public-facing modules |
 | `DESIGN.md` | Design decisions, rationale | Complex architectural decisions |

.cursorrules/error_handling.md

@@ -15,7 +15,7 @@ Standardized Git workflow ensures clean history, easy collaboration, and reliabl
 
 ```bash
 # ✅ GOOD: Descriptive feature branches
-git checkout -b feature/add-literature-search
+git checkout -b feature/add-reporting-dashboard
 git checkout -b feature/improve-pdf-validation
 git checkout -b bugfix/fix-rendering-crash
 
@@ -27,7 +27,7 @@ git checkout -b update
 
 ### Branch Naming Convention
 
-```
+```text
 <type>/<description>
 
 Types:
@@ -45,7 +45,7 @@ Types:
 
 ### Commit Message Format
 
-```
+```text
 <type>(<scope>): <description>
 
 [optional body]
@@ -57,7 +57,7 @@ Types:
 
 | Type | Description | Example |
 |------|-------------|---------|
-| `feat` | feature | `feat(literature): add arXiv search support` |
+| `feat` | feature | `feat(reporting): add HTML dashboard output` |
 | `fix` | Bug fix | `fix(pdf): resolve rendering crash on empty sections` |
 | `docs` | Documentation | `docs(api): update LLM integration guide` |
 | `style` | Code style | `style(core): format imports with isort` |
@@ -71,7 +71,7 @@ Types:
 ### Scopes
 
 - **infrastructure** - Infrastructure modules
-- **literature** - Literature search functionality
+- **reporting** - Reporting and dashboard generation
 - **llm** - LLM integration
 - **rendering** - Document rendering
 - **validation** - Quality validation
@@ -85,7 +85,7 @@ Types:
 
 ```bash
 # ✅ GOOD: Clear, descriptive commits
-feat(literature): add Semantic Scholar API integration
+feat(reporting): add executive summary generation
 
 - Implement Semantic Scholar source adapter
 - Add rate limiting for API calls
@@ -124,18 +124,21 @@ BREAKING CHANGE: ValidationError now requires context parameter
 ### Commit Message Guidelines
 
 #### Subject Line
+
 - **Limit to 50 characters**
 - **Start with lowercase** (except proper nouns)
 - **No period** at the end
 - **Imperative mood** ("add" not "added")
 
 #### Body (Optional)
+
 - **Separate from subject** with blank line
 - **Explain what and why**, not how
 - **Wrap at 72 characters**
 - **Use bullet points** for lists
 
 #### Footer (Optional)
+
 - **Breaking changes**: `BREAKING CHANGE: description`
 - **Issue references**: `Closes #123`, `Fixes #456`
 - **Co-authors**: `Co-authored-by: Name <email>`
@@ -429,6 +432,7 @@ Configure branch protection:
 ### Common Git Issues
 
 **Merge Conflicts:**
+
 ```bash
 # Abort merge
 git merge --abort
@@ -443,6 +447,7 @@ git rebase --continue
 ```
 
 **Lost Commits:**
+
 ```bash
 # Find lost commits
 git reflog
@@ -452,6 +457,7 @@ git checkout <commit-hash>
 ```
 
 **Large Files:**
+
 ```bash
 # Remove large files from history
 git filter-branch --tree-filter 'rm -f large-file.dat' HEAD
@@ -467,5 +473,5 @@ 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/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
+- [../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/folder_structure.md

@@ -8,7 +8,7 @@ The `infrastructure/` directory contains **reusable, generic build and validatio
 
 ### Subfolder Organization
 
-```
+```text
 infrastructure/<module>/
 ├── __init__.py           # Public API exports
 ├── AGENTS.md            # documentation
@@ -31,7 +31,7 @@ infrastructure/<module>/
 
 ### Test Organization
 
-```
+```text
 tests/infra_tests/test_<module>/
 ├── __init__.py
 ├── conftest.py          # Shared fixtures
@@ -53,29 +53,29 @@ tests/infra_tests/test_<module>/
 
 ```python
 # Good: Import from infrastructure package
-from infrastructure.literature import LiteratureSearch
+from infrastructure.reporting import generate_pipeline_report
 from infrastructure.llm import LLMClient
 from infrastructure.rendering import RenderManager
 from infrastructure.reporting import generate_pipeline_report, get_error_aggregator
 
 # Bad: Relative imports outside package
-from ..literature import LiteratureSearch  # DON'T
+from ..reporting import generate_pipeline_report  # DON'T
 ```
 
 ### Exception Handling
 
 ```python
 # Good: Use infrastructure exceptions
 from infrastructure.core.exceptions import (
-    LiteratureSearchError, 
+    ReportingError, 
     LLMConnectionError,
     RenderingError
 )
 
 # Good: Raise with context
-raise LiteratureSearchError(
-    "API request failed",
-    context={"source": "arxiv", "query": query}
+raise ReportingError(
+    "Report generation failed",
+    context={"format": "html", "stage": stage_name}
 )
 ```
 
@@ -93,12 +93,12 @@ logger.info(f"Processing {count} items")
 
 ## Module-Specific Guidelines
 
-### Literature Module
+### Documentation Module
 
-- **Multi-source**: Support multiple academic databases
-- **Rate limiting**: Respect API rate limits automatically
-- **Caching**: Cache responses where possible
-- **Deduplication**: Merge results from multiple sources
+- **Standards enforcement**: Validate AGENTS.md and README.md structure
+- **Cross-referencing**: Check internal link integrity
+- **Template generation**: Auto-generate documentation scaffolds
+- **Coverage tracking**: Monitor documentation completeness
 
 ### LLM Module
 
@@ -133,7 +133,7 @@ logger.info(f"Processing {count} items")
 
 ### Environment Variables
 
-- Prefix with module name: `LITERATURE_API_KEY`
+- Prefix with module name: `REPORTING_OUTPUT_DIR`
 - Document in module README.md
 - Provide sensible defaults
 
@@ -176,7 +176,7 @@ class ModuleConfig:
 
 ```python
 # Good
-raise LiteratureSearchError("Query failed")
+raise ReportingError("Report generation failed")
 
 # Bad
 raise Exception("Query failed")
@@ -188,7 +188,7 @@ raise Exception("Query failed")
 try:
     api_call()
 except RequestException as e:
-    raise LiteratureSearchError("API failed") from e
+    raise ReportingError("Report generation failed") from e
 ```
 
 ## Documentation Requirements
@@ -244,8 +244,9 @@ Infrastructure modules are integrated into the build pipeline through:
 5. **Validation** (`scripts/04_validate_output.py`) - Quality assurance
 
 **Pipeline Entry Points**: Two orchestrators available:
+
 - `./run.sh --pipeline`: 10 stages (0-9) with optional LLM stages (stage 0 cleanup, stages 1-9 tracked)
-- `python3 scripts/run_all.py`: 8-stage core pipeline (00-05) only
+- `python3 scripts/run_all.py`: 8-stage core pipeline (00-07) only
 
 Update these scripts to discover and use new infrastructure modules as needed.
 
@@ -258,7 +259,7 @@ Before committing:
 - [ ] AGENTS.md - [ ] README.md written
 - [ ] Type hints on all public APIs
 - [ ] Docstrings on all functions
-- [ ] infrastructure/__init__.py updated
+- [ ] infrastructure/**init**.py updated
 - [ ] infrastructure/AGENTS.md updated
 - [ ] No linter errors
 - [ ] Wrapper script created (if needed)
@@ -285,7 +286,7 @@ Before committing:
 
 ### Module Structure
 
-```
+```text
 infrastructure/example_module/
 ├── __init__.py           # Public API exports
 ├── core.py              # Core functionality
@@ -295,7 +296,7 @@ infrastructure/example_module/
 └── README.md            # Quick reference
 ```
 
-### __init__.py Example
+### **init**.py Example
 
 ```python
 """Example module - brief description.
@@ -465,20 +466,19 @@ Before merging a new infrastructure module:
 - [ ] Configuration documented
 - [ ] CLI interface working (if applicable)
 - [ ] No imports from project-specific code
-- [ ] infrastructure/__init__.py updated
+- [ ] infrastructure/**init**.py updated
 - [ ] infrastructure/AGENTS.md updated
 - [ ] Tests pass locally
 - [ ] No linter errors
 
 ## References
 
 - [Infrastructure AGENTS.md](../infrastructure/AGENTS.md) - Module organization
-- [Modules Guide](../docs/modules/MODULES_GUIDE.md) - guide to all advanced modules
-- [API Reference](../docs/reference/API_REFERENCE.md) - API documentation for all modules
-- [Two-Layer Architecture](../docs/architecture/TWO_LAYER_ARCHITECTURE.md) - Architecture explanation
+- [Modules Guide](../docs/modules/modules-guide.md) - guide to all advanced modules
+- [API Reference](../docs/reference/api-reference.md) - 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
 - [Documentation Guide](documentation_standards.md) - Writing module docs
 - [Type Hints Guide](type_hints_standards.md) - Type annotation patterns
-