enhance: improve filesystem & shell tools with pagination, fallback matching, and smarter output

[Re-bin]

Summary

Enhance the core filesystem and shell tools to close feature gaps identified by comparing with opencode's tool implementations.

Changes

ReadFileTool

• Added offset (1-indexed) and limit parameters for line-based pagination
• Output now includes line numbers in {n}| {content} format
• Character budget enforcement (_MAX_CHARS = 128K) trims from end when output is too large
• Pagination hints guide the LLM to continue reading (Use offset=N to continue)

EditFileTool

• Introduced progressive fallback matching via _find_match():
  1. Exact match
  2. Line-trimmed sliding window (handles indentation differences)
• CRLF line endings are detected via raw bytes and preserved through edits
• Added replace_all parameter for bulk replacements
• Ambiguous matches (count > 1) return a warning instead of silently replacing the wrong one
• "Not found" errors now show a diff against the best partial match (if >50% similar)

ListDirTool

• Added recursive mode using rglob("*") for deep directory exploration
• Added max_entries cap (default 200) with truncation message
• Built-in _IGNORE_DIRS set auto-skips .git, node_modules, __pycache__, .venv, etc.

ExecTool

• Output truncation changed from simple prefix cut to head + tail strategy, preserving both the beginning and end of long outputs
• Exposed timeout parameter to the LLM (1–600s), capped at _MAX_TIMEOUT
• Exit code is now always included in the output, not just on failure

Code quality

• Extracted _FsTool base class to eliminate duplicated __init__ and path resolution across all 4 filesystem tool classes
• Minor variable and naming cleanup for conciseness

Test plan

• All 246 tests passing (no regressions)
• New tests/test_filesystem_tools.py — 18 tests covering:
  • ReadFileTool: pagination, line numbers, offset bounds, empty file, char budget trimming
  • _find_match: exact, no-match, CRLF, line-trim fallback, multiple candidates
  • EditFileTool: exact edit, CRLF preservation, trim fallback, ambiguous warning, replace_all, not-found
  • ListDirTool: basic list, recursive, ignore dirs, max_entries truncation, empty dir, not-found
• Updated tests/test_tool_validation.py — 4 new tests covering:
  • ExecTool always returns exit code
  • Head+tail truncation for large outputs
  • Timeout parameter acceptance
  • Timeout capped at _MAX_TIMEOUT
• Zero lint errors on all modified files