merge: combine the v3 (ann/io/migrate) and v6 (agent/format) mission work

Two missions found largely disjoint ground — v3 in clawhdf5-ann, -io and
-migrate, v6 in -agent and -format — so this merge is mostly additive.

One genuine collision: BOTH runs independently implemented
`Dataset::verify_provenance` in clawhdf5/src/reader.rs, and git kept both,
producing `E0592 duplicate definitions`. They were functionally identical
apart from `self.file.data.as_bytes()` (v3) vs `self.file.as_bytes()` (v6).
Kept v6's — it is the variant that compiles against the current tree and
passed 52 suites, and its doc comment is the more honest one, stating both the
full-read cost and that an unkeyed hash stored beside its data is not a
tamper-evidence guarantee.

Verified present after the merge:
  P1  clawhdf5-ann now depends on clawhdf5-accel; compute_distance calls
      l2_distance / cosine_similarity instead of a scalar loop
  P2  AsyncFileReader caches its handle and length behind a mutex
  PR1 clawhdf5-migrate writes SHINES provenance, and validate checks it
  v6  WAL torn-tail truncation, char-boundary truncate, agent hardening

52 suites pass, 0 failures.

Co-Authored-By: Claude Opus 5 <[email protected]>

crates/clawhdf5-ann/Cargo.toml

@@ -12,6 +12,7 @@ categories = ["algorithms", "science"]
 [dependencies]
 clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
 clawhdf5-io = { path = "../clawhdf5-io", version = "2.1.0" }
+clawhdf5-accel = { path = "../clawhdf5-accel", version = "2.1.0" }
 rayon = { version = "1", optional = true }
 
 [features]

crates/clawhdf5-ann/src/hnsw.rs

@@ -44,32 +44,14 @@ impl DistanceMetric {
 }
 
 /// Compute distance between two vectors using the given metric.
+///
+/// Delegates to `clawhdf5-accel`'s runtime-dispatched SIMD kernels (AVX2 on
+/// x86_64, NEON on aarch64, portable scalar fallback elsewhere) — this is
+/// the hottest loop in both HNSW build and every `hybrid_search` query.
 fn compute_distance(a: &[f32], b: &[f32], metric: DistanceMetric) -> f32 {
     match metric {
-        DistanceMetric::L2 => {
-            let mut sum = 0.0f32;
-            for i in 0..a.len() {
-                let d = a[i] - b[i];
-                sum += d * d;
-            }
-            sum.sqrt()
-        }
-        DistanceMetric::Cosine => {
-            let mut dot = 0.0f32;
-            let mut norm_a = 0.0f32;
-            let mut norm_b = 0.0f32;
-            for i in 0..a.len() {
-                dot += a[i] * b[i];
-                norm_a += a[i] * a[i];
-                norm_b += b[i] * b[i];
-            }
-            let denom = norm_a.sqrt() * norm_b.sqrt();
-            if denom < f32::EPSILON {
-                1.0
-            } else {
-                1.0 - (dot / denom)
-            }
-        }
+        DistanceMetric::L2 => clawhdf5_accel::l2_distance(a, b),
+        DistanceMetric::Cosine => 1.0 - clawhdf5_accel::cosine_similarity(a, b),
     }
 }
 

crates/clawhdf5-io/src/async_read.rs

@@ -59,11 +59,16 @@ pub trait AsyncHDF5Read: Send + Sync {
 
 /// Async file-backed reader using tokio for non-blocking I/O.
 ///
-/// Opens a file and reads it asynchronously. The file is read into memory
-/// on first access, making subsequent operations fast.
+/// Opens a file and reads it asynchronously. The underlying file handle is
+/// opened once (lazily, on first access) and cached for the lifetime of this
+/// reader, so repeated granular `read_at` calls reuse the open descriptor
+/// and cached length instead of paying an open+stat syscall pair every time.
+/// The handle is guarded by a mutex, which also correctly serializes the
+/// seek-then-read pairs of concurrent callers sharing the one file position.
 #[derive(Debug)]
 pub struct AsyncFileReader {
     path: std::path::PathBuf,
+    handle: tokio::sync::Mutex<Option<(tokio::fs::File, u64)>>,
 }
 
 impl AsyncFileReader {
@@ -73,6 +78,7 @@ impl AsyncFileReader {
     pub fn new<P: AsRef<Path>>(path: P) -> Self {
         Self {
             path: path.as_ref().to_path_buf(),
+            handle: tokio::sync::Mutex::new(None),
         }
     }
 
@@ -89,23 +95,33 @@ impl AsyncFileReader {
 
 impl AsyncHDF5Read for AsyncFileReader {
     async fn read_at(&self, offset: u64, len: usize) -> io::Result<Vec<u8>> {
-        let mut file = tokio::fs::File::open(&self.path).await?;
-        let metadata = file.metadata().await?;
-        let file_len = metadata.len();
+        let mut guard = self.handle.lock().await;
+        if guard.is_none() {
+            let file = tokio::fs::File::open(&self.path).await?;
+            let file_len = file.metadata().await?.len();
+            *guard = Some((file, file_len));
+        }
+        let (file, file_len) = guard.as_mut().expect("just populated above");
+        let file_len = *file_len;
         if offset >= file_len {
             return Ok(Vec::new());
         }
         let available = (file_len - offset) as usize;
         let to_read = len.min(available);
-        tokio::io::AsyncSeekExt::seek(&mut file, io::SeekFrom::Start(offset)).await?;
+        tokio::io::AsyncSeekExt::seek(file, io::SeekFrom::Start(offset)).await?;
         let mut buf = vec![0u8; to_read];
         file.read_exact(&mut buf).await?;
         Ok(buf)
     }
 
     async fn len(&self) -> io::Result<u64> {
-        let metadata = tokio::fs::metadata(&self.path).await?;
-        Ok(metadata.len())
+        let mut guard = self.handle.lock().await;
+        if guard.is_none() {
+            let file = tokio::fs::File::open(&self.path).await?;
+            let file_len = file.metadata().await?.len();
+            *guard = Some((file, file_len));
+        }
+        Ok(guard.as_ref().expect("just populated above").1)
     }
 }
 

crates/clawhdf5-migrate/src/hdf5_reader.rs

@@ -49,6 +49,10 @@ pub fn read_hdf5(path: &str) -> Result<SqliteData, BoxErr> {
         entities,
         relations,
         embedding_dim,
+        // Not a SQLite read — the caller (incremental migration) carries
+        // forward the current run's actual `source_path` from the fresh
+        // SQLite read instead of using this placeholder.
+        source_path: String::new(),
     })
 }
 

crates/clawhdf5-migrate/src/hdf5_writer.rs

@@ -20,6 +20,7 @@ pub fn write_hdf5(
     opts: &WriteOptions,
 ) -> Result<(), Box<dyn std::error::Error>> {
     let mut builder = FileBuilder::new();
+    let timestamp = iso8601_now();
 
     // Root-level metadata attributes
     builder.set_attr("agent_id", AttrValue::String(opts.agent_id.clone()));
@@ -27,8 +28,18 @@ pub fn write_hdf5(
     builder.set_attr("embedding_dim", AttrValue::I64(data.embedding_dim as i64));
     builder.set_attr("source", AttrValue::String("sqlite-migration".into()));
     builder.set_attr("version", AttrValue::I64(1));
+    // Lineage: which SQLite database this output was migrated from and when,
+    // plus the migrator tool version — so a chain of `--incremental` runs
+    // still has an audit trail instead of every run overwriting the same
+    // static attributes (see research/03_provenance.md, INT-03).
+    builder.set_attr("source_path", AttrValue::String(data.source_path.clone()));
+    builder.set_attr("migrated_at", AttrValue::String(timestamp.clone()));
+    builder.set_attr(
+        "migrator_version",
+        AttrValue::String(env!("CARGO_PKG_VERSION").to_owned()),
+    );
 
-    write_chunks_group(&mut builder, data, opts);
+    write_chunks_group(&mut builder, data, opts, &timestamp);
     write_sessions_group(&mut builder, data);
     write_entities_group(&mut builder, data);
     write_relations_group(&mut builder, data);
@@ -37,6 +48,36 @@ pub fn write_hdf5(
     Ok(())
 }
 
+/// Current UTC time formatted as an ISO-8601 / RFC-3339 timestamp
+/// (`YYYY-MM-DDTHH:MM:SSZ`), with no external date/time dependency.
+fn iso8601_now() -> String {
+    let secs = std::time::SystemTime::now()
+        .duration_since(std::time::UNIX_EPOCH)
+        .unwrap_or_default()
+        .as_secs();
+    let days = (secs / 86_400) as i64;
+    let time_of_day = secs % 86_400;
+    let (h, m, s) = (time_of_day / 3600, (time_of_day % 3600) / 60, time_of_day % 60);
+    let (y, mo, d) = civil_from_days(days);
+    format!("{y:04}-{mo:02}-{d:02}T{h:02}:{m:02}:{s:02}Z")
+}
+
+/// Days-since-epoch to (year, month, day), Howard Hinnant's `civil_from_days`
+/// algorithm (proleptic Gregorian calendar, valid for the full `i64` range).
+fn civil_from_days(z: i64) -> (i64, u32, u32) {
+    let z = z + 719_468;
+    let era = if z >= 0 { z } else { z - 146_096 } / 146_097;
+    let doe = (z - era * 146_097) as u64; // [0, 146096]
+    let yoe = (doe - doe / 1460 + doe / 36_524 - doe / 146_096) / 365; // [0, 399]
+    let y = yoe as i64 + era * 400;
+    let doy = doe - (365 * yoe + yoe / 4 - yoe / 100); // [0, 365]
+    let mp = (5 * doy + 2) / 153; // [0, 11]
+    let d = (doy - (153 * mp + 2) / 5 + 1) as u32; // [1, 31]
+    let m = (if mp < 10 { mp + 3 } else { mp - 9 }) as u32; // [1, 12]
+    let y = if m <= 2 { y + 1 } else { y };
+    (y, m, d)
+}
+
 /// Build a fixed-length string Datatype from the max byte length of the items.
 fn string_dtype(max_len: usize) -> Datatype {
     Datatype::String {
@@ -66,7 +107,12 @@ fn apply_compression(ds: &mut clawhdf5_format::type_builders::DatasetBuilder, op
     }
 }
 
-fn write_chunks_group(builder: &mut FileBuilder, data: &SqliteData, opts: &WriteOptions) {
+fn write_chunks_group(
+    builder: &mut FileBuilder,
+    data: &SqliteData,
+    opts: &WriteOptions,
+    timestamp: &str,
+) {
     let mut group = builder.create_group("chunks");
     let n = data.chunks.len() as u64;
 
@@ -78,6 +124,16 @@ fn write_chunks_group(builder: &mut FileBuilder, data: &SqliteData, opts: &Write
 
     group.set_attr("count", AttrValue::I64(n as i64));
 
+    // Source attribution attached directly to the content-bearing datasets
+    // (SHA-256 of the raw bytes + creator/timestamp/source), so the chunk
+    // text and embeddings each carry their own verifiable provenance
+    // (see clawhdf5_format::provenance / `Dataset::verify_provenance`).
+    let source_opt = if data.source_path.is_empty() {
+        None
+    } else {
+        Some(data.source_path.as_str())
+    };
+
     // ids
     let ids: Vec<i64> = data.chunks.iter().map(|c| c.id).collect();
     group.create_dataset("id").with_i64_data(&ids);
@@ -87,7 +143,8 @@ fn write_chunks_group(builder: &mut FileBuilder, data: &SqliteData, opts: &Write
     let (text_raw, text_len) = pack_strings(&texts);
     group
         .create_dataset("text")
-        .with_compound_data(string_dtype(text_len), text_raw, n);
+        .with_compound_data(string_dtype(text_len), text_raw, n)
+        .with_provenance("clawhdf5-migrate", timestamp, source_opt);
 
     // embeddings - flatten to [N, dim]
     let dim = data.embedding_dim;
@@ -116,7 +173,8 @@ fn write_chunks_group(builder: &mut FileBuilder, data: &SqliteData, opts: &Write
         let ds = group
             .create_dataset("embeddings")
             .with_compound_data(f16_dtype, raw, n)
-            .with_shape(&[n, dim as u64]);
+            .with_shape(&[n, dim as u64])
+            .with_provenance("clawhdf5-migrate", timestamp, source_opt);
         apply_compression(ds, opts);
     } else {
         let flat: Vec<f32> = data
@@ -127,7 +185,8 @@ fn write_chunks_group(builder: &mut FileBuilder, data: &SqliteData, opts: &Write
         let ds = group
             .create_dataset("embeddings")
             .with_f32_data(&flat)
-            .with_shape(&[n, dim as u64]);
+            .with_shape(&[n, dim as u64])
+            .with_provenance("clawhdf5-migrate", timestamp, source_opt);
         apply_compression(ds, opts);
     }
 
@@ -274,3 +333,30 @@ fn write_relations_group(builder: &mut FileBuilder, data: &SqliteData) {
 
     builder.add_group(group.finish());
 }
+
+#[cfg(test)]
+mod time_tests {
+    use super::civil_from_days;
+
+    #[test]
+    fn epoch_day_zero_is_1970_01_01() {
+        assert_eq!(civil_from_days(0), (1970, 1, 1));
+    }
+
+    #[test]
+    fn known_dates_roundtrip() {
+        // 2026-08-16 is 20,681 days after 1970-01-01.
+        assert_eq!(civil_from_days(20_681), (2026, 8, 16));
+        // 2000-02-29 (leap day itself) and 2000-03-01 (the day after).
+        assert_eq!(civil_from_days(11_016), (2000, 2, 29));
+        assert_eq!(civil_from_days(11_017), (2000, 3, 1));
+    }
+
+    #[test]
+    fn iso8601_now_has_expected_shape() {
+        let ts = super::iso8601_now();
+        assert_eq!(ts.len(), "2026-08-16T00:00:00Z".len());
+        assert!(ts.starts_with("20")); // sanity: 21st-century year
+        assert!(ts.ends_with('Z'));
+    }
+}

crates/clawhdf5-migrate/src/main.rs

@@ -154,6 +154,10 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
             base.entities = source.entities;
             base.relations = source.relations;
             base.embedding_dim = source.embedding_dim.max(base.embedding_dim);
+            // Carry the current run's real SQLite source forward for
+            // provenance — `base` (re-read from the prior HDF5 output) has
+            // no meaningful source_path of its own.
+            base.source_path = source.source_path;
             if cli.verbose {
                 eprintln!("Incremental: appended {added} new chunks (id > {min_chunk_id})");
             }
@@ -199,6 +203,11 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         summary.embedding_dim,
         summary.rows_checked,
     );
+    if summary.provenance_verified {
+        eprintln!("Provenance: chunks/text and chunks/embeddings SHA-256 hashes verified.");
+    } else if cli.verbose {
+        eprintln!("Provenance: no provenance hash found to verify (older output format?).");
+    }
 
     Ok(())
 }

crates/clawhdf5-migrate/src/sqlite_reader.rs

@@ -51,6 +51,11 @@ pub struct SqliteData {
     pub entities: Vec<Entity>,
     pub relations: Vec<Relation>,
     pub embedding_dim: usize,
+    /// Filesystem path of the SQLite database this data was read from, for
+    /// provenance attribution on the HDF5 output. Empty when the data did
+    /// not come directly from a SQLite read (e.g. re-read of a prior HDF5
+    /// migration output for an incremental merge).
+    pub source_path: String,
 }
 
 /// A table name plus the ordered column names the reader maps by position.
@@ -225,6 +230,7 @@ pub fn read_sqlite_filtered(
         entities,
         relations,
         embedding_dim: dim,
+        source_path: path.to_owned(),
     })
 }
 

crates/clawhdf5-migrate/src/validate.rs

@@ -1,3 +1,6 @@
+use clawhdf5::reader::File as Hdf5File;
+use clawhdf5_format::provenance::VerifyResult;
+
 use crate::hdf5_reader::read_hdf5;
 use crate::sqlite_reader::SqliteData;
 
@@ -13,6 +16,12 @@ pub struct ValidationSummary {
     pub embedding_dim: u64,
     /// Number of rows whose full content was compared against the source.
     pub rows_checked: u64,
+    /// Whether the `chunks/text` and `chunks/embeddings` SHINES provenance
+    /// hashes (written via [`crate::hdf5_writer`]) were both present and
+    /// matched their recomputed SHA-256 on read-back. `false` when either
+    /// dataset has no provenance metadata (e.g. an older output file) or
+    /// there are zero chunks to check.
+    pub provenance_verified: bool,
 }
 
 /// Validate a migrated HDF5 file against the source data.
@@ -30,6 +39,7 @@ pub fn validate_hdf5(
     float16: bool,
 ) -> Result<ValidationSummary, BoxErr> {
     let got = read_hdf5(path)?;
+    let provenance_verified = verify_chunk_provenance(path)?;
 
     // ---- Counts ----
     check_count("chunk", got.chunks.len(), source.chunks.len())?;
@@ -126,6 +136,7 @@ pub fn validate_hdf5(
         relations: got.relations.len() as u64,
         embedding_dim: got.embedding_dim as u64,
         rows_checked,
+        provenance_verified,
     })
 }
 
@@ -136,6 +147,42 @@ fn check_count(kind: &str, got: usize, expected: usize) -> Result<(), BoxErr> {
     Ok(())
 }
 
+/// Re-verify the SHA-256 provenance hash of `chunks/text` and
+/// `chunks/embeddings` against their actual stored bytes, catching
+/// post-write corruption that a plain content comparison against the
+/// in-memory source wouldn't (the source is compared against what
+/// `read_hdf5` decoded, not against the raw bytes on disk).
+///
+/// Returns `Ok(true)` only if both datasets exist and both hashes match.
+/// Returns `Ok(false)` (not an error) if a dataset has no provenance
+/// attributes at all (e.g. a file written before this check existed) or
+/// there are zero chunks. Returns an error only on an actual hash mismatch —
+/// that indicates real corruption.
+fn verify_chunk_provenance(path: &str) -> Result<bool, BoxErr> {
+    let file = Hdf5File::open(path)?;
+    let Ok(chunks) = file.group("chunks") else {
+        return Ok(false);
+    };
+    let mut all_present = true;
+    for name in ["text", "embeddings"] {
+        let Ok(ds) = chunks.dataset(name) else {
+            all_present = false;
+            continue;
+        };
+        match ds.verify_provenance()? {
+            VerifyResult::Ok => {}
+            VerifyResult::NoHash => all_present = false,
+            VerifyResult::Mismatch { stored, computed } => {
+                return Err(format!(
+                    "provenance hash mismatch on chunks/{name}: stored {stored}, recomputed {computed} — data may be corrupted"
+                )
+                .into());
+            }
+        }
+    }
+    Ok(all_present)
+}
+
 fn field_err<T: std::fmt::Display>(kind: &str, i: usize, field: &str, s: T, g: T) -> BoxErr {
     format!("{kind}[{i}].{field} mismatch: source {s}, HDF5 {g}").into()
 }

crates/clawhdf5/src/reader.rs

@@ -426,6 +426,7 @@ impl<'f> Dataset<'f> {
         Ok(data_read::read_as_strings(&raw, &dt)?)
     }
 
+
     // ----- Selection-based read methods -----
 
     /// Read selected elements as raw bytes.

research/01_performance.md

@@ -0,0 +1,55 @@
+# Research: Performance — clawhdf5
+
+Scope: opportunities not already covered by the Tier 1-4 hardening passes
+recorded in `ROADMAP.md`/`CHANGELOG.md`/`IMPROVEMENT_LOG.md` (O(1) chunk
+cache, rayon-parallel `prune_connections`, workspace-hoisted deps, etc).
+
+## Finding P1 — HNSW's hot distance loop is scalar despite an existing SIMD crate
+
+**Location:** `crates/clawhdf5-ann/src/hnsw.rs:47-74` (`compute_distance`), called
+from `greedy_closest` and `search_layer` — the innermost loop of both index
+build and every `hybrid_search` query.
+
+**Problem:** `compute_distance` is a plain per-component `for i in 0..a.len()`
+scalar loop for both the `L2` and `Cosine` metrics. The workspace already ships
+`clawhdf5-accel` with runtime-dispatched AVX2/NEON/scalar-fallback
+`l2_distance`/`cosine_similarity` (`crates/clawhdf5-accel/src/lib.rs:125,148`),
+and `clawhdf5-agent` already depends on and uses it for its own linear cosine
+scan. `clawhdf5-ann/Cargo.toml` simply never lists `clawhdf5-accel` as a
+dependency, so the ANN crate — the one place with the tightest, most-called
+distance loop in the whole codebase — is the one place not using it.
+
+**Fix implemented (INT-01):** Added `clawhdf5-accel` as a dependency of
+`clawhdf5-ann` and rewired `compute_distance` to call
+`clawhdf5_accel::l2_distance` / `clawhdf5_accel::cosine_similarity` (mapping
+`1.0 - similarity` for the cosine-distance semantics the rest of the file
+expects). The accel crate already carries its own scalar fallback for
+platforms without AVX2/NEON, so no separate fallback branch is needed here.
+Existing `hnsw.rs` unit tests (build/search/serialize round-trip) validate
+behavior is unchanged; no format or public-API change.
+
+## Finding P2 — `AsyncFileReader::read_at` reopens and re-stats the file on every call
+
+**Location:** `crates/clawhdf5-io/src/async_read.rs:90-104`.
+
+**Problem:** Each `read_at` call does `tokio::fs::File::open` +
+`.metadata()` + `seek` + `read_exact` — two extra syscalls (open + stat) on
+every single granular read, with no persistent handle and no buffering. This
+directly defeats the purpose of the "chunked/granular async access" this type
+is documented for; callers doing many small reads (e.g. chunked dataset
+iteration) pay file-open overhead per chunk.
+
+**Fix implemented (INT-02):** `AsyncFileReader` now lazily opens the file
+once and caches the open handle (plus its length) behind a `tokio::sync::Mutex`,
+so subsequent `read_at`/`len` calls reuse the already-open descriptor instead
+of reopening. First call pays one open+stat; every call after is just a
+seek+read (or a length lookup with no syscall at all, since length is cached
+at open time). Behavior (including short-read truncation semantics) is
+unchanged and covered by the existing `async_file_reader_*` tests.
+
+## Not implemented — flagged for follow-up
+
+- **HNSW build-loop parallelism** (`hnsw.rs` insert loop) — ROADMAP already
+  notes this needs its own correctness-sensitive design pass (insert order
+  affects the graph, unlike `prune_connections`'s embarrassingly-parallel
+  per-node distance computation). Left as-is; out of scope for this pass.

research/02_security.md

@@ -0,0 +1,42 @@
+# Research: Security — clawhdf5
+
+Scope: opportunities not already covered by the shipped hardening (WAL CRC32
+trailer / `WAL_VERSION` 2, `MAX_WAL_FIELD_LEN` field caps, Android JNI length
+validation, `chunked_read.rs`/`data_read.rs` bounds-check + fuzz pass,
+decompression-bomb output bound, etc — see `ROADMAP.md`).
+
+## Finding S1 — WAL v2 still allocates untrusted field buffers before the CRC32 check runs
+
+**Location:** `crates/clawhdf5-agent/src/wal.rs`, entry read path
+(`read_len_prefixed_str`/`read_embedding` helpers feeding into the `Save`
+entry parser around lines 340-380; CRC verification happens afterward at
+~lines 246-255).
+
+**Problem:** Each `Save` entry currently contains three independent
+length-prefixed strings plus one length-prefixed embedding buffer. Each field
+is capped individually at `MAX_WAL_FIELD_LEN` (64 MiB) — but that cap is
+checked and then the buffer is **allocated immediately** as each field's
+length prefix is read, before the entry's trailing CRC32 is ever checked. A
+single corrupted entry (bit-flipped length prefixes) can therefore force up
+to ~4 allocations near 64 MiB each (~256 MB) before the CRC finally rejects
+it. This is exactly what `ROADMAP.md`'s "What's Next" section already flags
+as open: *"a stronger per-entry format (explicit length prefix, avoiding the
+read-then-verify restructuring) could still be revisited."*
+
+**Why not implemented in this pass:** Fixing this properly means a WAL format
+version bump (`WAL_VERSION` 3): frame each entry as one outer
+`[total_len: u32][entry_bytes][crc32: u32]`, read+CRC-check the whole raw
+entry buffer *first*, and only then parse the individual fields out of the
+already-verified buffer — mirroring the v1→v2 migration this file already
+does on open. That's a real, self-contained, well-testable change (the file
+already has a legacy-format migration test harness and corruption-detection
+tests to extend), but it touches the on-disk framing and the read/write pair
+needs to stay in lock-step, so it deserves its own dedicated
+implement-and-test pass rather than being bundled in alongside unrelated
+performance/provenance changes. Tracked as **INT-04** below for follow-up.
+
+## Finding S2 — no dataset-level integrity check on the agent memory read path
+
+See `research/03_provenance.md` finding PR2 (`INT-06`) — closely related to
+security (corruption detection on read), tracked there since the mechanism
+(`ProvenanceStore::verify_integrity`) is a provenance primitive.

research/03_provenance.md

@@ -0,0 +1,97 @@
+# Research: Provenance — clawhdf5
+
+Scope: data lineage, source attribution, and tamper-evidence for both the
+low-level HDF5 format layer and the higher-level agent-memory / migration
+tools built on top of it.
+
+## Finding PR1 — SHINES provenance (SHA-256 + creator/timestamp/source) is fully built and tested, but zero production write paths use it
+
+**Location:** `crates/clawhdf5-format/src/provenance.rs` (the whole module —
+`Provenance::build_attrs`, `sha256_hex`, `verify_dataset`) and
+`crates/clawhdf5-format/src/type_builders.rs:671-686`
+(`DatasetBuilder::with_provenance`, feature-gated on `provenance`, which is
+**on by default** in `clawhdf5-format`).
+
+**Problem:** This is a complete, working, already-tested feature — it writes
+`_provenance_sha256` / `_provenance_creator` / `_provenance_timestamp` /
+`_provenance_source` attributes on a dataset and can re-verify the hash later
+via `verify_dataset`. `grep -rl with_provenance crates/` shows it is
+exercised only by `clawhdf5-format`'s own tests/benches
+(`tests/robustness_tests.rs`, `tests/writer_h5py_tests.rs`,
+`benches/bench.rs`). Neither `clawhdf5-agent` (the memory backend) nor
+`clawhdf5-migrate` (the SQLite→HDF5 migration tool — the one place data
+crosses a genuine trust/source boundary) calls it. Concretely,
+`crates/clawhdf5-migrate/src/hdf5_writer.rs:24-28` sets only a handful of
+static root attributes (`agent_id`, `embedder`, `embedding_dim`, a *constant*
+`source="sqlite-migration"`, a *constant* `version=1`) — there is no source
+file path, no content hash of the source database, no migration timestamp,
+and `--incremental` runs (`main.rs` ~122-133) overwrite these same static
+attributes on every append, so a chain of incremental merges leaves no audit
+trail: a corrupted incremental append is indistinguishable after the fact
+from a clean one.
+
+**Fix implemented (INT-03):** Wired the *existing* SHINES provenance
+mechanism into the migration write path instead of inventing a new one:
+
+- `clawhdf5-migrate/src/hdf5_writer.rs`: the `embeddings` and `text` chunk
+  datasets are now built with `.with_provenance("clawhdf5-migrate", <RFC3339
+  timestamp>, Some(<source sqlite path>))`, so each migrated dataset carries
+  a verifiable SHA-256 of its own bytes plus who/when/where it came from.
+- `clawhdf5-migrate/src/sqlite_reader.rs`: `SqliteData` gained a
+  `source_path: String` field (the SQLite path actually read), threaded
+  through `read_sqlite_filtered`.
+- `clawhdf5-migrate/src/main.rs`: the incremental-merge arm now carries the
+  *current* run's `source_path` forward instead of silently keeping
+  whatever the previous run recorded.
+- `clawhdf5-migrate/src/validate.rs`: `validate_hdf5` now also calls
+  `clawhdf5_format::provenance::verify_dataset` on the embeddings dataset and
+  fails validation on a hash mismatch, so migration validation catches
+  post-write corruption, not just source/dest content drift.
+
+This directly closes the exact gap ROADMAP's "What's Next" implicitly left
+open (migration recorded no real lineage) using code that was already
+shipped, tested, and sitting unused one crate over — no new format version,
+no new dependency, minimal blast radius (2 struct-literal sites for the new
+`SqliteData` field, both updated).
+
+## Finding PR2 — agent-level `MemoryProvenance`/`AnomalyDetector` are dead code on the real save path (ROADMAP claims Track 5 "complete")
+
+**Location:** `crates/clawhdf5-agent/src/lib.rs` (`HDF5Memory::save` /
+`save_batch`, ~lines 538-572); `crates/clawhdf5-agent/src/provenance.rs`
+(`MemoryProvenance`, `ProvenanceStore::verify_integrity`/`mark_verified`);
+`crates/clawhdf5-agent/src/anomaly.rs` (`AnomalyDetector::check_rate_anomaly`
+/ `check_pattern_anomaly` / `check_source_anomaly`).
+
+**Problem:** `ROADMAP.md` Track 5 ("Memory Security & Provenance") is marked
+🟢 Complete, but `save()`/`save_batch()` push straight into the in-memory
+cache + WAL without ever constructing a `MemoryProvenance` record, without
+ever calling any `AnomalyDetector` check, and without going through
+`SourceIsolation`. A `grep` for `provenance::`/`anomaly::` usage across the
+crate turns up only each module's own `#[cfg(test)]` block. So today a
+forged- or poisoned-source memory write is stored and later retrieved with
+zero attribution and zero anomaly screening, contradicting the shipped-status
+claim in the docs.
+
+**Why not implemented in this pass:** This is a real fix, but it is
+core-save-path surgery — it has to interact correctly with the WAL replay
+path (a provenance record written to cache but not WAL, or vice versa, would
+silently desync memory from the durable log on crash-recovery) and with
+`save_batch`'s different code path from `save`. That needs its own focused
+implement-and-test pass with the existing `provenance.rs`/`anomaly.rs` unit
+tests as a base, rather than being bundled in under time pressure alongside
+unrelated changes. Tracked as **INT-05** below.
+
+## Finding PR3 — nothing on the retrieval path ever calls `verify_integrity`
+
+**Location:** `crates/clawhdf5-agent/src/provenance.rs:128`
+(`ProvenanceStore::verify_integrity`), vs. `search.rs`/`hybrid.rs` (no
+callers).
+
+**Problem:** Even independent of PR2, nothing in the retrieval pipeline
+calls `verify_integrity` before returning a chunk to the caller, so
+corruption of stored chunk text is retrievable and usable without any check
+ever running.
+
+**Why not implemented in this pass:** Blocked on PR2/INT-05 landing first —
+`verify_integrity` needs a `MemoryProvenance` record to check *against*, and
+none are currently produced. Tracked as **INT-06**, sequenced after INT-05.