Enhance git add to support batch operations and deletions

[MementoRC]

Problem Description

The current mcp__git__git_add tool has significant limitations that make it difficult to handle common git workflows:

Current Issues:

1. ❌ Cannot add deleted files - Returns "Files not found" error
2. ❌ No batch operation support - No equivalent to git add -A or git add -u
3. ❌ Requires explicit file paths - No wildcard or pattern support
4. ❌ Cannot stage directory deletions - Manual workarounds required

Observed Error Example:

❌ Files not found: reports/health_score.txt, reports/maintenance_needed.txt, reports/project_health.json

Proposed Solution

Extend existing tool with new parameters:

mcp__git__git_add({
  repo_path: string,
  files?: string[],              // existing
  add_all?: boolean,             // equivalent to git add -A
  update_only?: boolean,         // equivalent to git add -u
  include_deletions?: boolean,   // handle deleted files
  patterns?: string[]            // glob patterns like "*.py"
})

Use Cases

1. CI Fix Workflows

// Stage all changes including deletions (common in CI cleanup)
mcp__git__git_add({repo_path: ".", add_all: true})

// Stage only tracked file updates and deletions
mcp__git__git_add({repo_path: ".", update_only: true})

2. Cleanup Operations

// Stage deletion of temporary files
mcp__git__git_add({
  repo_path: ".", 
  files: ["reports/temp.txt", "cache/old.json"], 
  include_deletions: true
})

Impact

This was the primary blocker during a recent CI fix session, forcing workarounds like:

• Manual file deletion instead of proper git staging
• Using bash commands, defeating MCP integration benefits
• Complex multi-step operations for simple batch adds

Implementation Notes

• Maintain backward compatibility with existing files parameter
• Add validation for conflicting parameters (e.g., add_all + files)
• Provide clear error messages for invalid combinations

Related

• Complements git clean support (Add git clean support for __pycache__ directories #24)