Strip atlassian-mcp-server to bare bones for local use

## Issue Description

The forked atlassian-mcp-server contains many files that aren't essential for local-only usage. To reduce token usage when AI agents read the codebase, we should strip it down to its bare functional bones.

## Files to Remove

### Distribution/Publishing Infrastructure
- `Dockerfile` - containerization not needed for local use
- `smithery.yaml` - Smithery.ai registry configuration
- PyPI metadata in `pyproject.toml` (keep only dependency management)
- `uv.lock` - 251KB dependency lock file

### Community/Documentation Files
- `CONTRIBUTING.md` - contributor guidelines
- `SECURITY.md` - security policy
- `AGENTS.md` - AI agents documentation
- Original `README.md` (32KB) - we have `README.dotfiles.md`

### Testing Infrastructure (if not needed)
- `tests/` directory and all test files
- Test dependencies in `pyproject.toml`
- Any pytest configuration files

## Additional Investigation Needed

While removing the above files, also search for and consider removing:

1. **CI/CD configurations**:
- Any GitHub Actions workflows
- GitLab CI files
- Other CI configuration files

2. **Documentation**:
- API documentation files
- Example configurations (except those needed locally)
- Changelog files
- Any `docs/` directories

3. **Development tools**:
- Linting configurations (`.flake8`, `.pylintrc`, etc.)
- Pre-commit hooks
- Editor-specific files beyond `.gitignore`
- Makefile (if not used for local setup)

4. **Package metadata**:
- `MANIFEST.in`
- `setup.cfg`
- Any `*.egg-info` directories
- Version files not used by the code

5. **Example/Demo files**:
- Sample configurations
- Demo scripts
- Tutorial content

## Goal

Keep only the absolute minimum needed to:
- Run the MCP server locally
- Install dependencies
- Configure for personal Atlassian instances

Essential files to keep:
- `src/` directory (core functionality)
- Minimal `pyproject.toml` (dependencies only)
- `setup.sh` and essential scripts
- `.gitignore`
- `LICENSE`
- `README.dotfiles.md` or a minimal README

## Benefits

- Significantly reduce token usage for AI agents
- Faster codebase comprehension
- Less clutter when navigating
- Focus on actual functionality

## Context

This follows the principle of "subtraction creates value" - removing non-essential files makes the codebase more focused and efficient for its intended local-only use case.

Inventory the repository against the listed removal candidates, starting with pyproject.toml, setup.sh, the src/ directory, and any CI, documentation, testing, or packaging files found by the investigation. Check which files are required to install, configure, and run the Atlassian MCP server locally. Done means local setup still works with only the retained essentials and unnecessary distribution, community, testing, and development files are removed.

Written by the indexing model from the issue text.