Refactor: Update MCP server for research management

[Brad-Edwards]

Description

Update the MCP (Model Context Protocol) server tools to reflect the new research management domain. Rename all tool prefixes from gc_ to gs_ and replace requirements-oriented tools with research-oriented tools.

Scope

• Rename all MCP tool prefixes from gc_ to gs_
• Remove requirements-specific tools (e.g., gc_create_requirement, gc_list_requirements, etc.)
• Add research paper tools: gs_create_paper, gs_list_papers, gs_search_papers, gs_create_citation, etc.
• Add experiment tools: gs_create_experiment, gs_transition_experiment, gs_list_experiments, etc.
• Add research note tools: gs_create_note, gs_list_notes, gs_search_notes, etc.
• Update tool descriptions and parameter schemas
• Update any MCP server configuration

Acceptance Criteria

• All tools use gs_ prefix
• No gc_ prefixed tools remain
• Paper management tools functional
• Experiment management tools functional
• Research note tools functional
• MCP server starts and registers all tools correctly