fix(tools): address PR review — remove _extract_raw_output, BudgetConfig everywhere, read_file hardening

- Remove _extract_raw_output: persist content verbatim (fixes size mismatch bug)
- Drop import aliases: import from budget_config directly, one canonical name
- BudgetConfig param on maybe_persist_tool_result and enforce_turn_budget
- read_file: limit=None signature, pre-read guard fires only when limit omitted (256KB)
- Unify binary extensions: file_operations.py imports from binary_extensions.py
- Exclude .pdf and .svg from binary set (text-based, agents may inspect)
- Remove redundant outer try/except in eval path (internal fallback handles it)
- Fix broken tests: update assertion strings for new persistence format
- Module-level constants: _PRE_READ_MAX_BYTES, _DEFAULT_READ_LIMIT
- Remove redundant pathlib import (Path already at module level)
- Update spec.md with IMPLEMENTED annotations and design decisions

tools/registry.py

@@ -176,8 +176,8 @@ class ToolRegistry:
             return entry.max_result_size_chars
         if default is not None:
             return default
-        from tools.tool_result_storage import DEFAULT_MAX_RESULT_SIZE_CHARS
-        return DEFAULT_MAX_RESULT_SIZE_CHARS
+        from tools.budget_config import DEFAULT_RESULT_SIZE_CHARS
+        return DEFAULT_RESULT_SIZE_CHARS
 
     def get_all_tool_names(self) -> List[str]:
         """Return sorted list of all registered tool names."""