fix: handle declaration merging and function overloads correctly

[TonyStef]

Summary

• Declaration merging: interface User { name } + interface User { age } — removing one declaration now correctly flags as modified (not deleted), since User still exists via the other declaration.
• Deduplication: Deleted files with multiple declarations of the same symbol produce one deletion entry, not one per declaration.
• Signature comparison: Uses group-based comparison (sorted signature sets) instead of comparing individual old symbols against a single Map entry. Prevents false modification flags.
• Function overloads: Overload signatures (without body) aren't extracted by tree-sitter — only the implementation is tracked. Removing an overload while keeping the implementation is correctly invisible. Documented in test.

Test plan

• 58/58 tests pass (2 new integration tests)
• Typecheck clean
• Biome lint clean
• Build clean