[MCP Error] git_add fails on deleted files

**Tool:**
mcp__git__git_add

**Expected behavior:**
Should stage deleted files just like standard `git add` command

**Actual behavior:**
Returns error: "Files not found in repository: mcp/tool-discovery.md" when trying to stage a deleted file

**Error message:**
```
Error: Tool execution failed: Files not found in repository: mcp/tool-discovery.md
```

**Context:**
Was trying to stage changes including a deleted file (mcp/tool-discovery.md) along with modified files. The standard git behavior allows staging deleted files.

**Workaround used:**
Used bash command `git add mcp/tool-discovery.md` which worked correctly

**Reproduction:**
1. Delete a file from the repository
2. Try to stage it with `mcp__git__git_add`
3. Observe the error

**Expected fix:**
The tool should detect deleted files and handle them appropriately, similar to how git add works natively.