fix: correct run.sh script parameters and disable HNSW code (v0.3.1)

- Fix syntax error in run.sh: remove extra quote and correct --log-path to --log-file
- Comment out HNSW algorithm implementation in enc.rs and algorithms.rs to simplify codebase
- Bump version to 0.3.1 in Cargo.toml
- Remove HNSW implementation guide and test files
- Add comprehensive project writeup documentation

run.sh

@@ -20,4 +20,4 @@ chmod +x "${SCRIPT_DIR}/test"
 "${SCRIPT_DIR}/test" \
 	--dataset "$DATASET_FILE" \
 	--predictions "$PREDICTIONS_RESULT_FILE" \
-	--log-path "/home/admin/workspace/job/logs/user.log'"
+	--log-file "/home/admin/workspace/job/logs/user.log"