Package structure and docs updated

[Vybornak2]

Updated structure to align with new architecture.
Updated docs, docs settings for compatibility.

[Copilot]

Pull Request Overview

This PR restructures and updates the documentation configuration to align with the new architecture and improve compatibility. Key changes include updating the MkDocs configuration (with revised theme palette and markdown extensions), reorganizing API and developer documentation, and adding new JavaScript files for MathJax and table sorting.

Reviewed Changes

Copilot reviewed 35 out of 35 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
mkdocs.yml	Revised theme settings, updated markdown extension list, and new plugins to support improved documentation navigation and theming.
docs/theory/index.md	Updated the API Reference link to reflect the new documentation structure.
docs/javascripts/*.js	Added new JavaScript files for MathJax and table sorting functionality.
docs/index.md	Updated contact email formatting and added front matter.
Documentation files (CONTRIBUTING.md, CODE_OF_CONDUCT.md, etc.)	Replaced inline content with external file references for consistency.
API docs files (utilities.md, data_parsing.md, core/*, etc.)	Removed files to reflect the restructured API documentation.
.vscode/settings.json	Added MkDocs-specific YAML settings for improved editor support.
.vscode/extensions.json	Updated extension list to include YAML support.

[codecov-commenter]

Welcome to Codecov 🎉

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

ℹ️ You can also turn on project coverage checks and project coverage reporting on Pull Request comment

Thanks for integrating Codecov - We've got you covered ☂️

[Copilot]

Pull Request Overview

This PR updates the documentation structure for FatPy to align with the new architecture and improve compatibility. Key changes include:

• Adding YAML frontmatter and standardized metadata to various documentation files.
• Updating the inclusion of license, contributing, and code of conduct documents via file includes.
• Removing several API documentation files, likely as part of the overall restructuring, and updating VS Code settings and extensions for MkDocs compatibility.

Reviewed Changes

Copilot reviewed 40 out of 40 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
docs/index.md	Added frontmatter and updated contact email formatting
docs/faber_cost.md	Added new documentation page with frontmatter
docs/development/license.md	Replaced full license text with an include directive
docs/development/index.md	Updated contact email formatting in developer documentation
docs/development/contributing.md	Collapsed documentation via include directive
docs/development/code_of_conduct.md	Collapsed documentation via include directive
docs/api/utilities.md	Removed file as part of the updated API documentation structure
docs/api/index.md	Replaced extensive API content with minimal frontmatter and options
docs/api/data_parsing.md	Removed the Data Parsing API documentation
docs/api/core/stress_life.md	Removed the Stress Life module documentation
docs/api/core/strain_life.md	Removed the Strain Life module documentation
docs/api/core/index.md	Removed the Core Modules documentation
docs/api/core/energy_life.md	Removed the Energy Life module documentation
CONTRIBUTING.md	Updated contact email formatting in contributing guidelines
.vscode/settings.json	Added MkDocs-related YAML schema and custom tag settings
.vscode/extensions.json	Updated VS Code extensions with YAML support and autodocstring updates

Comments suppressed due to low confidence (6)

docs/api/data_parsing.md:1

• [nitpick] Verify that the removal of the Data Parsing documentation is intentional and that corresponding references have been updated accordingly.

# Data Parsing

docs/api/core/stress_life.md:1

• [nitpick] Confirm that the removal of the Stress Life module documentation aligns with the planned API restructuring and that consumers are informed of where to find the updated references.

# Stress Life Module

docs/api/core/strain_life.md:1

• [nitpick] Confirm that the removal of the Strain Life module documentation is part of the intended API update and ensure that the new structure provides equivalent guidance.

# Strain Life Module

docs/api/core/index.md:1

• [nitpick] Check that the removal of the Core Modules documentation does not leave API navigation incomplete and that the new documentation structure adequately covers these components.

# Core Modules

docs/api/core/energy_life.md:1

• [nitpick] Ensure that the removal of the Energy Life module documentation is intentional and that any relocation or replacement is clearly referenced for users.

# Energy Life Module

docs/development/license.md:5

• Ensure that the include directive correctly references the LICENSE.md file and that the file exists at the expected location.

--8<-- "LICENSE.md"