Adds think, checkpoint, and flag tools for agent reasoning visibility:
- think: records observation/hypothesis/next_action before investigation
- checkpoint: summarizes learned/unknown/next_phase after file clusters
- flag: marks notable findings to flags.jsonl with severity levels
Additional changes:
- Step numbering in investigation system prompt
- Text blocks from agent now printed to stderr (step labels visible)
- flag tool available in both investigation and synthesis passes
- analyze_directory() returns (brief, detailed, flags) three-tuple
- format_flags() in report.py renders flags sorted by severity
- Per-directory max_turns increased from 10 to 14
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Adds --ai flag that sends the directory tree, file categories, and
sampled file contents to Claude for analysis. Produces a brief
summary at the top of the report and a detailed breakdown at the
end. Requires ANTHROPIC_API_KEY env var; degrades gracefully without it.
Uses only stdlib (urllib) to keep the zero-dependency constraint.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Human-readable terminal report with clear sections, plus JSON output
mode and file output support.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
