Updated README.md and HOWTOUSE.md with explicit directory guidance after
multiple users reported confusion about installation process.
Changes:
- Split Quick Start into clear two-step process (install tool vs analyze project)
- Added explicit warnings about which directory to use for each command
- Added directory structure diagram showing tool vs project separation
- Added Common Issues & Troubleshooting section with solutions for:
- Missing .pf/manifest.json error
- Tree-sitter not available warning
- Installation timeout errors
- Nested virtual environment problems
- Emphasized NOT creating venv before installing TheAuditor
- Added clear ❌ and ✅ markers for common mistakes
This addresses user confusion about:
- Where to install TheAuditor (tools dir, not project)
- Where to run commands from (project dir for analysis)
- Why nested venvs break things (don't create your own)
- Which Python to use (system, not venv)