🐛 Bug: GitHub init creates helper files without .sh extension

## 🐛 Bug Report

### Description
The `npx claude-flow@alpha github init` command appears to be creating helper files without the `.sh` extension, causing execution failures.

### Error Message
```
Stop [./.claude/helpers/github-checkpoint-hooks.sh session-end] failed with non-blocking status code 127:
/bin/sh: 1: ./.claude/helpers/github-checkpoint-hooks.sh: not found
```

### Expected Behavior
The command should create:
- `.claude/helpers/github-checkpoint-hooks.sh` (with .sh extension)
- Other helper files with proper extensions

### Actual Behavior
It appears the files are being created without the `.sh` extension, causing the shell to be unable to find/execute them.

### Steps to Reproduce
1. Run `npx claude-flow@alpha github init`
2. Check the `.claude/helpers/` directory
3. Observe that helper files may be missing the `.sh` extension
4. Hook execution fails with "not found" error

### Potential Fix
The init command should ensure all shell script helper files are created with the proper `.sh` extension:
- `github-checkpoint-hooks.sh`
- `checkpoint-manager.sh`
- `standard-checkpoint-hooks.sh`

### Environment
- Claude Flow version: v2.0.0-alpha.81
- OS: Various (reported on Linux)
- Shell: sh/bash

### Impact
- Hooks fail to execute
- GitHub integration features don't work
- Users get confusing "not found" errors

### Priority
High - This breaks the GitHub integration feature

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**Labels**: bug, github-integration, high-priority