feat: packed single-file embedding index (closes #3)

The semantic index was ~90 896 per-entry files (index/embeddings/<safe-model>/
<sha256>.f32), a deployment liability: the file count — not the 356 MB — is
hostile to container layers, object storage, and Git-LFS, and Pipeline::load
opened every one individually. This packs a complete per-file store into one
self-describing matrix file loaded in a single read.

New src/packed.rs owns the format: 4-byte magic "AIPK", u32 LE format_version,
u32 LE header length, a JSON PackedHeader {n_rows, dim, embed_model,
corpus_sha256, corpus_name}, pad to a 4-byte boundary, then row-major
little-endian f32 payload in corpus order (row i = corpus entry i). write_packed
is atomic (temp+rename); read_packed rejects a wrong magic, a newer-than-
supported version, a malformed header, or a payload length inconsistent with
n_rows×dim. corpus_sha256 hashes the raw corpus file bytes.

Pipeline::load now calls a free fn load_packed_or_store(cfg, entries) that
prefers the packed file and falls back to today's all-or-nothing per-file store,
reporting which path it took via a new IndexStatus {Ok, Absent, Mismatch}
carried into Diagnostics. `alpha-id index --pack` writes the file from a
complete store (refusing an incomplete one with exit 2), recording corpus_sha256
+ embed_model in the header as the artifact-binding data.

Iteration boundary (deliberate): this is iteration 1 of the packed-versioned-
bundle cycle. load_packed_or_store validates the packed file STRUCTURALLY only
(magic/version/payload length via read_packed, plus n_rows == entries.len());
it does NOT yet compare the header's corpus_sha256/embed_model against the live
config, and IndexStatus::Mismatch fires only on structural corruption. The
load-time mismatch warning, the index= token on the diagnostics line, and the
Hybrid-degrade-names-reason wiring are iteration 2 (issue #4), which consumes
the binding data this commit writes. The per-file store is untouched — it stays
the build/resume path; the packed file is an additive serve-path artifact.

mmap was considered and rejected: the brute-force full-scan cosine search
touches every row per query, so memory-mapping yields no runtime benefit over a
single read and would add an unsafe dependency (spec § Out of scope).

Verification: cargo test green (61 tests; 9 new — 3 format round-trip/hash/bad-
magic, 4 load-path incl. packed-beats-store and structural n_rows mismatch, 2
--pack CLI incl. exit-2 refusal). An end-to-end seam test writes the packed
file via the CLI, removes the per-file store, and asserts the pipeline builds
its index from the packed file alone as IndexStatus::Ok (#3 acceptance b).

Spec: docs/specs/2026-05-31-packed-versioned-index-bundle.md
Plan: docs/plans/2026-06-01-packed-versioned-bundle-iter1.md

closes #3

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

tests/pack_cli_tests.rs

@@ -0,0 +1,122 @@
+use alpha_id::model::{AlphaIdEntry, Config, IndexStatus};
+use alpha_id::pipeline::load_packed_or_store;
+use std::path::Path;
+use std::process::Command;
+
+// Write a minimal config TOML pointing the corpus + index dir at temp paths.
+// The `--pack` branch only reads `alpha_id_path` (corpus) and `index_dir`
+// (store); `claml_path` etc. are present for parse but unused on this path.
+fn write_config(dir: &Path, corpus: &Path, index_dir: &Path) -> std::path::PathBuf {
+    let toml = format!(
+        r#"ionos_base_url = "http://127.0.0.1:1"
+token_path = "/nonexistent"
+embed_model = "test/model"
+rerank_model = "test/rerank"
+alpha_id_path = "{corpus}"
+claml_path = "/nonexistent.xml"
+index_dir = "{index}"
+pool_size = 10
+top_k = 10
+"#,
+        corpus = corpus.to_str().unwrap(),
+        index = index_dir.to_str().unwrap(),
+    );
+    let p = dir.join("config.toml");
+    std::fs::write(&p, toml).unwrap();
+    p
+}
+
+fn corpus_line(text: &str) -> String {
+    // Alpha-ID format: valid|alpha_id|primary|star|addon|primary2|orpha|text
+    format!("1|A0001|A00|||||{text}")
+}
+
+#[test]
+fn pack_refuses_incomplete_store_exit_2() {
+    let dir = tempfile::tempdir().unwrap();
+    let corpus = dir.path().join("corpus.txt");
+    std::fs::write(&corpus, format!("{}\n{}\n", corpus_line("alpha"), corpus_line("beta"))).unwrap();
+    let index_dir = dir.path().join("index");
+    std::fs::create_dir_all(&index_dir).unwrap();
+    let config = write_config(dir.path(), &corpus, &index_dir);
+
+    let out = Command::new(env!("CARGO_BIN_EXE_alpha-id"))
+        .args(["--config", config.to_str().unwrap(), "index", "--pack"])
+        .output()
+        .unwrap();
+    assert_eq!(out.status.code(), Some(2), "incomplete store must exit 2");
+    let stderr = String::from_utf8_lossy(&out.stderr);
+    assert!(stderr.contains("store incomplete"), "stderr was: {stderr}");
+}
+
+#[test]
+fn pack_writes_file_from_complete_store() {
+    let dir = tempfile::tempdir().unwrap();
+    let corpus = dir.path().join("corpus.txt");
+    std::fs::write(&corpus, format!("{}\n{}\n", corpus_line("alpha"), corpus_line("beta"))).unwrap();
+    let index_dir = dir.path().join("index");
+    std::fs::create_dir_all(&index_dir).unwrap();
+
+    // Populate the per-file store for both entry texts so the pack succeeds.
+    let store = alpha_id::embed::EmbeddingStore::open(index_dir.to_str().unwrap(), "test/model").unwrap();
+    store.put("alpha", &[1.0f32, 0.0]).unwrap();
+    store.put("beta", &[0.0f32, 1.0]).unwrap();
+
+    let config = write_config(dir.path(), &corpus, &index_dir);
+    let out = Command::new(env!("CARGO_BIN_EXE_alpha-id"))
+        .args(["--config", config.to_str().unwrap(), "index", "--pack"])
+        .output()
+        .unwrap();
+    assert!(out.status.success(), "stderr: {}", String::from_utf8_lossy(&out.stderr));
+    let packed = index_dir.join("packed.test_model.bin");
+    assert!(packed.exists(), "packed file should be written at {}", packed.display());
+}
+
+fn entry(text: &str) -> AlphaIdEntry {
+    AlphaIdEntry {
+        alpha_id: "A0001".to_string(),
+        valid: true,
+        icd_primary: "A00".to_string(),
+        icd_star: String::new(),
+        icd_addon: String::new(),
+        icd_primary2: String::new(),
+        orpha: String::new(),
+        text: text.to_string(),
+    }
+}
+
+/// End-to-end seam: a packed file produced by the `index --pack` CLI loads back
+/// through the production `load_packed_or_store` path as `IndexStatus::Ok` with a
+/// usable index, with no per-file store consulted. This pins the cross-boundary
+/// round trip (CLI writer ↔ pipeline reader) that the two halves' unit tests
+/// each cover only one side of.
+#[test]
+fn cli_packed_file_loads_back_as_ok_index() {
+    let dir = tempfile::tempdir().unwrap();
+    let corpus = dir.path().join("corpus.txt");
+    std::fs::write(&corpus, format!("{}\n{}\n", corpus_line("alpha"), corpus_line("beta"))).unwrap();
+    let index_dir = dir.path().join("index");
+    std::fs::create_dir_all(&index_dir).unwrap();
+
+    let store = alpha_id::embed::EmbeddingStore::open(index_dir.to_str().unwrap(), "test/model").unwrap();
+    store.put("alpha", &[1.0f32, 0.0]).unwrap();
+    store.put("beta", &[0.0f32, 1.0]).unwrap();
+
+    let config = write_config(dir.path(), &corpus, &index_dir);
+    let out = Command::new(env!("CARGO_BIN_EXE_alpha-id"))
+        .args(["--config", config.to_str().unwrap(), "index", "--pack"])
+        .output()
+        .unwrap();
+    assert!(out.status.success(), "stderr: {}", String::from_utf8_lossy(&out.stderr));
+
+    // Load the CLI-written packed file through the production path. The store
+    // directory is removed first to prove the index comes from the packed file
+    // alone, not the per-file store.
+    std::fs::remove_dir_all(index_dir.join("embeddings")).unwrap();
+    let mut cfg = Config::load(config.to_str().unwrap()).unwrap();
+    cfg.index_dir = index_dir.to_str().unwrap().to_string();
+    let entries = vec![entry("alpha"), entry("beta")];
+    let (vector, status) = load_packed_or_store(&cfg, &entries);
+    assert!(vector.is_some(), "packed file written by the CLI must yield an index");
+    assert_eq!(status, IndexStatus::Ok);
+}

tests/packed_load_tests.rs

@@ -0,0 +1,73 @@
+use alpha_id::model::{AlphaIdEntry, Config, IndexStatus};
+use alpha_id::packed::{packed_path, write_packed, PackedHeader};
+use alpha_id::pipeline::load_packed_or_store;
+
+fn entry(text: &str) -> AlphaIdEntry {
+    AlphaIdEntry {
+        alpha_id: "X".to_string(),
+        valid: true,
+        icd_primary: "A00".to_string(),
+        icd_star: String::new(),
+        icd_addon: String::new(),
+        icd_primary2: String::new(),
+        orpha: String::new(),
+        text: text.to_string(),
+    }
+}
+
+fn cfg_in(dir: &std::path::Path) -> Config {
+    let mut cfg = Config::load("config/default.toml").unwrap();
+    cfg.index_dir = dir.to_str().unwrap().to_string();
+    cfg.embed_model = "test/model".to_string();
+    cfg
+}
+
+#[test]
+fn index_status_defaults_to_absent() {
+    assert_eq!(IndexStatus::default(), IndexStatus::Absent);
+}
+
+#[test]
+fn index_status_serializes_externally_tagged() {
+    let j = serde_json::to_string(&IndexStatus::Mismatch("x".to_string())).unwrap();
+    assert!(j.contains("Mismatch"), "got {j}");
+}
+
+#[test]
+fn packed_beats_store_builds_without_store() {
+    let dir = tempfile::tempdir().unwrap();
+    let cfg = cfg_in(dir.path());
+    let entries = vec![entry("a"), entry("b")];
+    let rows = vec![vec![1.0f32, 0.0], vec![0.0f32, 1.0]];
+    let h = PackedHeader {
+        n_rows: 2,
+        dim: 2,
+        embed_model: cfg.embed_model.clone(),
+        corpus_sha256: "irrelevant-in-iter1".to_string(),
+        corpus_name: "c.txt".to_string(),
+    };
+    write_packed(&packed_path(&cfg.index_dir, &cfg.embed_model), &h, &rows).unwrap();
+    // No per-file store populated in `dir`; the index must come from the packed file.
+    let (vector, status) = load_packed_or_store(&cfg, &entries);
+    assert!(vector.is_some());
+    assert_eq!(status, IndexStatus::Ok);
+}
+
+#[test]
+fn n_rows_mismatch_yields_mismatch_none() {
+    let dir = tempfile::tempdir().unwrap();
+    let cfg = cfg_in(dir.path());
+    let entries = vec![entry("a"), entry("b"), entry("c")]; // 3 entries
+    let rows = vec![vec![1.0f32, 0.0], vec![0.0f32, 1.0]]; // packed claims 2 rows
+    let h = PackedHeader {
+        n_rows: 2,
+        dim: 2,
+        embed_model: cfg.embed_model.clone(),
+        corpus_sha256: "x".to_string(),
+        corpus_name: "c.txt".to_string(),
+    };
+    write_packed(&packed_path(&cfg.index_dir, &cfg.embed_model), &h, &rows).unwrap();
+    let (vector, status) = load_packed_or_store(&cfg, &entries);
+    assert!(vector.is_none());
+    assert!(matches!(status, IndexStatus::Mismatch(_)));
+}

tests/packed_tests.rs

@@ -0,0 +1,46 @@
+use alpha_id::packed::{corpus_sha256, read_packed, write_packed, PackedHeader};
+use std::io::Write;
+
+fn header(n_rows: u32, dim: u32) -> PackedHeader {
+    PackedHeader {
+        n_rows,
+        dim,
+        embed_model: "test/model".to_string(),
+        corpus_sha256: "deadbeef".to_string(),
+        corpus_name: "corpus.txt".to_string(),
+    }
+}
+
+#[test]
+fn write_read_roundtrip_preserves_header_and_rows() {
+    let dir = tempfile::tempdir().unwrap();
+    let path = dir.path().join("packed.bin");
+    let rows = vec![vec![0.0f32, 1.5, -2.25], vec![3.0, 4.0, 5.0]];
+    let h = header(2, 3);
+    write_packed(&path, &h, &rows).unwrap();
+    let (got_h, got_rows) = read_packed(&path).unwrap();
+    assert_eq!(got_h, h);
+    assert_eq!(got_rows, rows);
+}
+
+#[test]
+fn corpus_sha256_stable_and_sensitive() {
+    let dir = tempfile::tempdir().unwrap();
+    let p = dir.path().join("c.txt");
+    std::fs::write(&p, b"alpha|beta").unwrap();
+    let a = corpus_sha256(p.to_str().unwrap()).unwrap();
+    let b = corpus_sha256(p.to_str().unwrap()).unwrap();
+    assert_eq!(a, b, "same bytes hash identically");
+    std::fs::write(&p, b"alpha|betb").unwrap();
+    let c = corpus_sha256(p.to_str().unwrap()).unwrap();
+    assert_ne!(a, c, "one changed byte changes the hash");
+}
+
+#[test]
+fn read_packed_rejects_bad_magic() {
+    let dir = tempfile::tempdir().unwrap();
+    let path = dir.path().join("bad.bin");
+    let mut f = std::fs::File::create(&path).unwrap();
+    f.write_all(b"XXXX____________").unwrap();
+    assert!(read_packed(&path).is_err());
+}