fix(migrate): write a real clawhdf5-agent store

clawhdf5-migrate wrote a layout of its own (/chunks, /sessions,
/entities, /relations, root attributes, no /meta or schema_version) that
HDF5Memory::open rejects, so a "migrated" SQLite database could not be
used as agent memory — contrary to the README.

It now writes through the agent's own API (HDF5Memory::create/open,
save_batch, the session cache and the knowledge graph), so there is no
second copy of the schema:

- sessions and entities/relations carry over; deleted rows become
  deleted records (or are left out with --skip-deleted);
- embeddings follow the library default (float16), --f32 opts out and
  --float16 is a hidden no-op, as in clawhdf5-cli; the `half`-based
  conversion is gone;
- every source row is checked before the output is created: a wrong
  embedding length, an empty embedding, a dimension that differs from
  an existing store's, or a float16 value beyond +-65504 is an error
  naming the chunk id, and an existing store is left untouched;
- --incremental opens the existing store, adds only rows it does not
  hold (matched by content) and follows the source's deleted flags;
- a source with no memory rows needs --embedding-dim;
- validation reads the result back with HDF5Memory::open_read_only,
  compares every field (embeddings bit for bit, round_to_f16 of the
  source for float16) and checks a migrated record is found by search.

clawhdf5-agent gains HDF5Memory::sessions()/sessions_mut(),
HDF5Memory::delete_batch (one save, all-or-nothing, no auto-compact),
SessionCache::add_at, and re-exports SessionCache/SessionEntry.

The old layout's per-dataset SHA-256 provenance attributes have no place
in the agent schema and are gone. An adversarial review found two
blockers (silent truncation of long embeddings; an --incremental
dimension check that could never fire) and four majors (a failed run
wiping the existing store, dim-0 stores, deleted-flag drift); all are
fixed with regression tests. 42 migrate tests, incl. h5py opening a
migrated store.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>

crates/clawhdf5-migrate/README.md

@@ -3,9 +3,12 @@
 [![crates.io](https://img.shields.io/crates/v/clawhdf5-migrate.svg)](https://crates.io/crates/clawhdf5-migrate)
 [![docs.rs](https://img.shields.io/docsrs/clawhdf5-migrate)](https://docs.rs/clawhdf5-migrate)
 
-CLI tool to migrate SQLite agent memory databases to HDF5 format.
+CLI tool to migrate SQLite agent memory databases (the ZeroClaw layout) to a
+[clawhdf5-agent](https://crates.io/crates/clawhdf5-agent) store.
 
-Converts existing SQLite-based agent memory stores (embeddings, text chunks, metadata) into the HDF5 format used by [clawhdf5-agent](https://crates.io/crates/clawhdf5-agent).
+The output is written through `clawhdf5-agent`'s own API, so it opens with
+`HDF5Memory::open` and is searchable immediately: memory records, sessions and
+the knowledge graph (entities and relations) are carried over.
 
 ## Installation
 
@@ -16,9 +19,19 @@ cargo install clawhdf5-migrate
 ## Usage
 
 ```bash
-clawhdf5-migrate --input agent.db --output agent.h5
+clawhdf5-migrate --sqlite agent.db --hdf5 agent.h5 --agent-id my-agent
 ```
 
+Embeddings are stored as float16 (the library default for new stores); pass
+`--f32` for full precision. Every embedding must have the same dimension
+(the first row's, or `--embedding-dim`, which a source with no memory records
+requires); rows are never truncated, and the whole source is checked before an
+existing output store is replaced. `--incremental` adds only new rows to an
+existing store of the same dimension and carries over changes to rows'
+deleted flags, `--skip-deleted` leaves out tombstoned rows, and `--dry-run`
+only counts.
+See `clawhdf5-migrate --help` for every option.
+
 ## License
 
 MIT