Migrate to uv; fix clippings paths and wrapper

README.md

@@ -30,20 +30,28 @@ ssearch/
 ├── clippings/                  # Symlink to clippings (PDFs, TXT, webarchive, RTF)
 ├── store/                      # Persisted journal vector store
 ├── models/                     # Cached HuggingFace models (offline)
-├── requirements.txt            # Python dependencies
+├── pyproject.toml              # Project metadata and dependencies (uv)
+├── uv.lock                     # Pinned dependency lockfile (uv)
 ```
 
 ## Setup
 
-**Prerequisites**: Python 3.12, [Ollama](https://ollama.com) with `gemma4:e4b` or similar pulled.
+**Prerequisites**: [uv](https://docs.astral.sh/uv/), [Ollama](https://ollama.com) with `gemma4:e4b` or similar pulled. uv manages the Python 3.12 toolchain and dependencies.
 
 ```bash
 cd ssearch
-python3 -m venv .venv
-source .venv/bin/activate
-pip install -r requirements.txt
+uv sync                    # create .venv and install the search pipeline
+uv sync --group notebook   # also install Jupyter / analysis deps (optional)
 ```
 
+`uv sync` reads `pyproject.toml` and the pinned `uv.lock`, creating `.venv` automatically (no manual `python -m venv` or activation needed). Run any script with `uv run`:
+
+```bash
+uv run python retrieve.py "your query"
+```
+
+You can still `source .venv/bin/activate` and call `python` directly if you prefer.
+
 The `data/` symlink should point to the journal archive (plain `.txt` files). The `clippings/` symlink should point to the clippings folder. The embedding model (`BAAI/bge-large-en-v1.5`) and cross-encoder (`cross-encoder/ms-marco-MiniLM-L-12-v2`) are cached in `./models/` for offline use.
 
 ### Offline model loading