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

Cargo.lock

@@ -410,7 +410,7 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "hfe_knn"
-version = "0.3.0"
+version = "0.3.1"
 dependencies = [
  "anyhow",
  "bincode 2.0.1",