Circular symlink keeps appearing: commands/templates/templates

## Problem
A circular symlink is repeatedly being created at `commands/templates/templates` that points to its parent directory:
```
commands/templates/templates -> ../commands/templates
```

## Observed Behavior
- The symlink appears as an untracked file in `git status`
- It has been manually removed multiple times with `rm commands/templates/templates`
- The symlink reappears later, suggesting something is recreating it

## Impact
- Clutters git status output
- Requires manual cleanup before committing
- Risk of accidentally committing the circular symlink

## When Observed
This has been seen multiple times across different work sessions, including:
- During work on issue #1049 (git MCP pyproject.toml fix)
- During work on issue #1055 (MCP debugging improvements)

## Potential Sources
The symlink might be created by:
- `setup.sh` or one of its subscripts
- Command generation scripts in `.claude/`
- `utils/generate-claude-commands.sh`
- An IDE or development tool

## Next Steps
Need to investigate which script or tool is creating this circular symlink and fix the root cause.

Inspect setup.sh and its subscripts, the command-generation scripts under .claude/, and utils/generate-claude-commands.sh for creation of commands/templates/templates. Trace which script or tool recreates the symlink, then verify the root cause is fixed by removing it and confirming it does not reappear in git status.

Written by the indexing model from the issue text.