fix: resolve critical bugs causing crashes and silent errors

[Sumit4codes]

• Add error handling for JSON.parse in RPC system to prevent worker crashes
• Fix array bounds checking in websearch/codesearch tools
• Add proper server shutdown handling in TUI worker
• Replace empty catch blocks with proper error logging
• Add bounds checking before array access in edit tools
• Fix parseInt radix usage in snapshot and storage modules

These fixes prevent application crashes from malformed input and improve error visibility.