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/file_operations.py

@@ -33,6 +33,7 @@ from dataclasses import dataclass, field
 from typing import Optional, List, Dict, Any
 from pathlib import Path
 from hermes_constants import get_hermes_home
+from tools.binary_extensions import BINARY_EXTENSIONS
 
 
 # ---------------------------------------------------------------------------
@@ -280,26 +281,6 @@ class FileOperations(ABC):
 # Shell-based Implementation
 # =============================================================================
 
-# Binary file extensions (fast path check)
-BINARY_EXTENSIONS = {
-    # Images
-    '.png', '.jpg', '.jpeg', '.gif', '.webp', '.bmp', '.ico', '.tiff', '.tif',
-    '.svg',  # SVG is text but often treated as binary
-    # Audio/Video
-    '.mp3', '.mp4', '.wav', '.avi', '.mov', '.mkv', '.flac', '.ogg', '.webm',
-    # Archives
-    '.zip', '.tar', '.gz', '.bz2', '.xz', '.7z', '.rar',
-    # Documents
-    '.pdf', '.doc', '.docx', '.xls', '.xlsx', '.ppt', '.pptx',
-    # Compiled/Binary
-    '.exe', '.dll', '.so', '.dylib', '.o', '.a', '.pyc', '.pyo', '.class',
-    '.wasm', '.bin',
-    # Fonts
-    '.ttf', '.otf', '.woff', '.woff2', '.eot',
-    # Other
-    '.db', '.sqlite', '.sqlite3',
-}
-
 # Image extensions (subset of binary that we can return as base64)
 IMAGE_EXTENSIONS = {'.png', '.jpg', '.jpeg', '.gif', '.webp', '.bmp', '.ico'}