Add remaining git commands to MCP server (config, ls-files, init, clone, submodule)

## Summary
Following the implementation of essential git commands in #712/#713, this issue tracks the remaining "nice to have" git commands that would complete our git MCP server implementation.

## Remaining Commands to Implement

### 1. **`git ls-files`** - List tracked files
- Show files under version control
- Different from regular `ls` - only shows git-tracked files
- Useful for scripting and automation
- Read-only operation

### 2. **`git config`** - Get/set configuration values
- Support both get and set operations
- Handle --global, --local, --system scopes
- Common in setup scripts and automation
- Both read and write operations

### 3. **`git init`** - Initialize new repository
- Create new git repository
- Support --bare flag
- Less common in batch operations but fundamental
- Write operation

### 4. **`git clone`** - Clone repositories
- Clone from URLs or local paths
- Handle authentication if possible
- Support common flags (--depth, --branch, etc.)
- Useful for multi-repo automation
- Write operation

### 5. **`git submodule`** - Manage submodules
- Most complex - multiple subcommands needed:
- init, update, add, remove, status, foreach
- Important for projects using submodules
- Both read and write operations

## Implementation Notes

Each command should follow the established pattern:
- BaseModel class for parameters
- GitTools enum entry
- Function implementation with error handling
- Addition to TOOL_REGISTRY
- Proper categorization in READ_ONLY_TOOLS or WRITE_TOOLS
- Support in git_batch with shorthand mapping
- Case handling in call_tool

## Priority Order (by complexity)
1. `git ls-files` - Simplest, read-only
2. `git config` - Straightforward get/set
3. `git init` - Simple write operation
4. `git clone` - Moderate complexity (URL/auth handling)
5. `git submodule` - Most complex (multiple actions)

## Related
- Previous issues: #706, #712
- PRs: #711, #713

This would complete the git MCP server implementation with all commonly used git commands.

Start with the established BaseModel pattern, GitTools enum, TOOL_REGISTRY, READ_ONLY_TOOLS, WRITE_TOOLS, git_batch shorthand mapping, and call_tool handling mentioned in the issue. Work through the commands in the stated priority order, beginning with git ls-files. Done means all five command groups and their listed operations are registered, categorized, batch-supported, and have error handling.

Written by the indexing model from the issue text.