feat: enhance code search and visualization tools#13
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- Added `search_code` tool for full-text search over indexed files, replacing traditional grep. - Introduced `trace_calls` tool to analyze call graphs, providing insights into function interactions. - Updated `find_symbol` tool to support natural-language queries alongside exact names and regex patterns. - Enhanced Atlas visualization to include new node types (`method`) and link kinds (`extends`, `implements`). - Improved rendering logic for nodes and links in the Atlas view, adjusting sizes and colors for better clarity. - Updated API types to include new symbol kinds and link types, ensuring consistency across the application.
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search_codetool for full-text search over indexed files, replacing traditional grep.trace_callstool to analyze call graphs, providing insights into function interactions.find_symboltool to support natural-language queries alongside exact names and regex patterns.method) and link kinds (extends,implements).