refactor: rename runtime folders with underscore prefix

Rename folders to follow Python convention for internal/private:
- log/ → _log/ (runtime logs, debugging)
- output/ → _output/ (runtime results, user downloads)
- input/ → _input/ (user testing files, not app input)

Rationale: _ prefix signals "internal, temporary, not part of public API"

Updated files:
- src/agent/llm_client.py - Path("log") → Path("_log")
- src/tools/youtube.py - Path("log") → Path("_log")
- test/test_phase0_hf_vision_api.py - Path("output") → Path("_output")
- .gitignore - Updated folder references (log/, input/ → _log/, _input/, added _output/)
- CHANGELOG.md - Added infrastructure entry

Co-Authored-By: Claude <noreply@anthropic.com>

.gitignore

@@ -28,17 +28,20 @@ uv.lock
 Thumbs.db
 
 # Input documents (PDFs not allowed in HF Spaces)
-input/*.pdf
-input/
+_input/*.pdf
+_input/
 
-# Downloaded GAIA question files
-input/*
+# Downloaded GAIA question files (user testing)
+_input/*
 
 # Runtime cache (not in git, served via app download)
 _cache/
 
 # Runtime logs (not in git, for debugging and analysis)
-log/
+_log/
+
+# Runtime results (not in git, for user download)
+_output/
 
 # Testing
 .pytest_cache/

CHANGELOG.md

@@ -1,5 +1,37 @@
 # Session Changelog
 
+## [2026-01-13] [Infrastructure] [COMPLETED] Runtime Folder Naming Convention - Underscore Prefix
+
+**Problem:** Folders `log/`, `output/`, and `input/` didn't clearly indicate they were runtime-only storage, making it unclear which folders are internal vs permanent.
+
+**Solution:** Renamed all runtime-only folders to use `_` prefix, following Python convention for internal/private.
+
+**Folders Renamed:**
+- `log/` → `_log/` (runtime logs, debugging)
+- `output/` → `_output/` (runtime results, user downloads)
+- `input/` → `_input/` (user testing files, not app input)
+
+**Rationale:**
+- `_` prefix signals "internal, temporary, not part of public API"
+- Consistent with Python convention (`_private`, `__dunder__`)
+- Distinguishes runtime storage from permanent project folders
+- `_cache/` already followed this convention ✓
+
+**Updated Files:**
+- **src/agent/llm_client.py** - `Path("log")` → `Path("_log")`
+- **src/tools/youtube.py** - `Path("log")` → `Path("_log")`
+- **test/test_phase0_hf_vision_api.py** - `Path("output")` → `Path("_output")`
+- **.gitignore** - Updated folder references
+
+**Git Status:**
+- Old folders removed from git tracking
+- New folders excluded by .gitignore
+- Existing files in those folders become untracked
+
+**Result:** Clear separation between runtime storage (`_` prefix) and permanent project folders (no prefix)
+
+---
+
 ## [2026-01-13] [Infrastructure] [COMPLETED] Session Log Consolidation - Single File Per Run
 
 **Problem:** Each question created a separate log file (`llm_context_TIMESTAMP.txt`), polluting the log/ folder with 20+ files per evaluation.

src/agent/llm_client.py

@@ -75,7 +75,7 @@ def get_session_log_file() -> Path:
     global _SESSION_LOG_FILE
 
     if _SESSION_LOG_FILE is None:
-        log_dir = Path("log")
+        log_dir = Path("_log")
         log_dir.mkdir(exist_ok=True)
 
         # Create session filename with timestamp

src/tools/youtube.py

@@ -62,7 +62,7 @@ def save_transcript_to_cache(video_id: str, text: str, source: str) -> None:
         source: "api" or "whisper"
     """
     try:
-        log_dir = Path("log")
+        log_dir = Path("_log")
         log_dir.mkdir(exist_ok=True)
 
         cache_file = log_dir / f"{video_id}_transcript.txt"

test/test_phase0_hf_vision_api.py

@@ -364,7 +364,7 @@ if __name__ == "__main__":
         from datetime import datetime
 
         timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
-        output_dir = Path("output")
+        output_dir = Path("_output")
         output_dir.mkdir(exist_ok=True)
 
         output_file = output_dir / f"phase0_vision_validation_{timestamp}.json"