Fork mcp-atlassian into dotfiles for self-hosted Atlassian support

## Problem

The `mcp-atlassian` tool claims to support self-hosted Atlassian instances (Server/Data Center) but appears to have incomplete implementation. While authentication succeeds after our fix to use `--confluence-personal-token` and `--jira-personal-token`, API calls fail with permission errors or return empty results.

## Evidence of Issues

1. Authentication works (no more 401 errors) but API calls fail
2. `jira_get_all_projects` returns empty array instead of projects
3. `jira_get_user_profile` returns permission denied errors
4. Direct curl tests suggest the tool may not handle self-hosted auth flows correctly (session cookies, different API endpoints, etc.)

## Proposed Solution

Fork the `mcp-atlassian` source code into our dotfiles repository to:

1. **Debug and fix self-hosted support** - Add proper session handling, cookie support, and API compatibility
2. **Customize for our environment** - Tailor it specifically for self-hosted instances behind corporate auth
3. **Maintain control** - No longer dependent on upstream fixes or waiting for PRs to be merged
4. **Add features** - Implement organization-specific functionality as needed

## Implementation Steps

1. Find the source repository for `mcp-atlassian`
2. Fork/copy the code into `mcp/servers/atlassian-mcp-server/`
3. Update the wrapper script to use our local version instead of `uvx mcp-atlassian`
4. Set up the development environment (Python, dependencies, etc.)
5. Debug and fix the self-hosted authentication/API issues
6. Add logging to understand the auth flow better

## Benefits

- Full control over the implementation
- Ability to add detailed logging for debugging
- Can fix issues immediately without waiting for upstream
- Can add organization-specific features (custom fields, workflows, etc.)
- Follows our "building from source" philosophy for better control

## References

- Original tool installed via: `uvx mcp-atlassian`
- Docker image alternative: `ghcr.io/sooperset/mcp-atlassian:latest`
- Current wrapper: `mcp/atlassian-mcp-wrapper.sh`

Start with mcp/atlassian-mcp-wrapper.sh and compare its uvx mcp-atlassian invocation with the upstream source and the documented personal-token options. Reproduce jira_get_all_projects and jira_get_user_profile against the self-hosted instance, then trace the API and authentication behavior. Done means the local server is wired into the wrapper and those calls work with the required self-hosted configuration.

Written by the indexing model from the issue text.