refactor: deprecate tools that duplicate Claude Code built-in capabilities

[BumpyClock]

Summary

After testing all 15 LSP-MCP tools for their value to LLM coding agents, 3 tools were identified as duplicating functionality already available in Claude Code's built-in tools.

Problem

LLM coding agents like Claude Code already have robust file operations tools:

• Glob - Fast file pattern matching
• LS - Directory listing
• Read - File reading with line numbers
• Grep - Content search with regex support

Having LSP-MCP tools that duplicate these capabilities:

1. Bloats the tool list - 15 tools creates decision paralysis for LLMs
2. Wastes context - Tool descriptions take up prompt space
3. Creates confusion - Multiple ways to do the same thing
4. No additional value - The LSP versions aren't semantically-aware for these operations

Tools to Deprecate

1. list_files

• Current: Returns files in the workspace
• Duplicates: Glob with pattern **/* or LS command
• LSP advantage: None - both are simple file listing

2. read_source_code

• Current: Reads source code with optional range
• Duplicates: Read tool with offset/limit parameters
• LSP advantage: None - Read already provides line numbers and range selection

3. find_identifier

• Current: Finds identifiers by name in a file
• Duplicates: Grep with the identifier name as pattern
• LSP advantage: Minimal - could use AST but current implementation appears text-based

Proposed Changes

Option A: Remove from all presets (Recommended)

Remove these tools from minimal, standard, and full presets. They remain available for explicit opt-in via config.

{
  "minimal": ["definitions_in_file", "hover", "get_diagnostics"],
  "standard": ["definitions_in_file", "find_definition", "find_references", "hover", "workspace_symbol", "get_diagnostics"],
  "full": ["definitions_in_file", "find_definition", "find_references", "hover", "workspace_symbol", "get_diagnostics", "outgoing_calls", "incoming_calls", "go_to_implementation"]
}

Option B: Mark as deprecated

Add deprecation warnings to tool descriptions:

"[DEPRECATED: Use Glob/Read tools instead] Lists files in the workspace"

Impact

• Reduces default tool count from 15 to 12 (or fewer with other consolidations)
• Cleaner tool interface for LLM agents
• No loss of functionality - capabilities remain via built-in tools

Related

• Full tool analysis: .ai_agents/tool_review.md
• Issue feat: reduce output noise in find_references and definitions_in_file #138: Output noise improvements