Update CLAUDE.md and link to existing documentation

[jonpspri]

Summary

• Reorganize CLAUDE.md with clearer structure and documentation quick links
• Enable flake8 and black in pre-commit hooks for consistent code quality
• Standardize use of uv environment manager across Makefile and CI
• Configure Neovim linters (flake8, pylint) for editor integration
• Fix pytest warnings configuration in test runs

Changes

Documentation Improvements

• Restructure CLAUDE.md with focused essential commands section
• Move detailed performance configuration to dedicated docs
• Add comprehensive documentation quick links section organized by category
• Clarify uv usage for virtual environment management

Code Quality Tooling

• Enable flake8 pre-commit hook for style enforcement
• Enable black pre-commit hook for consistent formatting
• Remove obsolete fix-encoding-pragma hook
• Configure Neovim ALE linters: mypy, ruff, flake8, pylint

Build System Updates

• Add make uv target to ensure uv is installed (brew or curl fallback)
• Update make pylint to use uv run with proper error handling
• Adjust make test to show warnings (remove --disable-warnings)
• Standardize pylint flags: --fail-on E --fail-under 10

CI/CD Alignment

• Install uv in GitHub Actions lint workflow
• Update pylint job to use uv run instead of pip install
• Ensure CI matches local development environment

Test Plan

• Run make venv install-dev - virtual environment setup works
• Run make flake8 - linting passes
• Run make pylint - pylint checks pass with uv
• Run make black - formatting applied correctly
• Run make pre-commit - all pre-commit hooks execute
• Run make test - tests pass with warnings visible
• Verify GitHub Actions lint workflow completes

[Copilot]

Pull Request Overview

This PR standardizes development tooling around uv as the environment manager and improves documentation organization. The changes focus on aligning local development workflows with CI/CD, enabling consistent code quality checks, and making documentation more discoverable through better organization and quick links.

Key changes:

• Standardize on uv for environment management across Makefile, CI workflows, and documentation
• Enable flake8 and black pre-commit hooks while removing obsolete encoding pragma hook
• Reorganize CLAUDE.md with focused essential commands and comprehensive documentation quick links

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
Makefile	Add uv installation target, update pylint to use uv run, remove --disable-warnings from pytest
CLAUDE.md	Restructure with clearer sections, move performance details to dedicated docs, add documentation quick links
.pre-commit-config.yaml	Enable flake8 and black hooks, remove fix-encoding-pragma hook
.nvim.lua	Add flake8 and pylint to ALE linters configuration
.github/workflows/lint.yml	Install uv in CI, update pylint job to use uv run instead of pip install

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[jonpspri]

Also, a note before we commit. AGENTS.md seems to be where the non-proprietary crowd are headed for Code Agent context (see, for example, https://pnote.eu/notes/agents-md/#agentsmd-becomes-the-convention). Shall we consolidate on AGENTS.md and symlink CLAUDE.md and GEMINI.md to that? (The existing AGENTS.md seems more focused toward the llms.md crowd...)