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/binary_extensions.py

@@ -16,8 +16,8 @@ BINARY_EXTENSIONS = frozenset({
     # Executables/binaries
     ".exe", ".dll", ".so", ".dylib", ".bin", ".o", ".a", ".obj", ".lib",
     ".app", ".msi", ".deb", ".rpm",
-    # Documents (PDF is here; read_file excludes it at the call site)
-    ".pdf", ".doc", ".docx", ".xls", ".xlsx", ".ppt", ".pptx",
+    # Documents (exclude .pdf — text-based, agents may want to inspect)
+    ".doc", ".docx", ".xls", ".xlsx", ".ppt", ".pptx",
     ".odt", ".ods", ".odp",
     # Fonts
     ".ttf", ".otf", ".woff", ".woff2", ".eot",