…efs GH-219)

Round 24: Zero SATD across all 3 projects (36 violations eliminated).
F-PROFILE-010 fixed: apr qa now reports Ollama parity letter grade.
Bugs #117-120. Popperian Score: 192/206 (93.2%), 12 FALSIFIED.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…-SHIP2-009)

GATE-ARCH-370M-004 gains evidence_discharged_by + discharge_status:
PARTIAL_ALGORITHM_LEVEL. Three algorithm-level invariants wired without
training:

  1. Coverage — every 370M tensor (219 entries: 1 embed + 1 lm_head +
     9 per-layer × 24 layers + 1 final norm) resolves to a
     TensorContract entry in LayoutContract::new(). Pattern-normalises
     per-layer names; any uncovered tensor would be silently skipped
     by GGUF export.

  2. Row-major ordering (INV-ARCH-370M-009) — every 2D shape is
     [out_dim, in_dim]. Pinned lm_head/embed/q_proj/k_proj shapes
     verify GQA (k_proj = [kv_heads*head_dim, hidden]) and bind the
     370M architecture to the GH-202-regression-proof layout.

  3. Critical-tensor enforcement — validate_apr_shape accepts
     [vocab, hidden] AND rejects reversed [hidden, vocab] on
     lm_head.weight. Proves the validator catches layout bugs, not
     just passes silently.

Full discharge (GGUF cosine-parity on trained 370M, max_logit_cosine
≤ 1e-3 over 100 canary prompts) blocks on compute-dispatch
(AC-SHIP2-003/004). Harness is fixture-swap-ready once a trained .apr
exists — no test rewrite needed. Spec §9 Risk #2 names this exact
mitigation path.

Contract: llama-370m-sovereign-v1.yaml v1.2.0 → v1.3.0, stays ACTIVE.
Tests: 2 new test fns in crates/aprender-train/src/models/llama_370m.rs
(8/8 pass). `pv validate` = 0 errors, 0 warnings.

Closes #117. Binds to AC-SHIP2-009 / FALSIFY-SHIP-019.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

…tone

Records the SHIP-019 algorithm-level PARTIAL discharge (task #117,
commit 846cc1d) in the authoritative spec:

- Version bump 2.21.0 → 2.22.0
- Full amendment block #4 under post-v2.19 evidence window documenting
  GATE-ARCH-370M-004 wired to `layout_contract.rs` algorithm proofs
  (219-tensor coverage + row-major ordering + GH-202 rejection)
- New "counter-example hunting" pattern lesson: prior "exhausted
  PARTIAL levers" verdict was ~86% correct; re-running the 7-gate
  FALSIFY-SHIP survey with explicit counter-example hunting found
  exactly one genuine lever (SHIP-019). SHIP-017/018/020 need compute;
  SHIP-013/014/016 collapse into SHIP-011 wiring.
- Combined MODEL-2 ledger: 3/12 fully ACTIVE + 3/12 PARTIAL = 6/12
  touched (50%). Remaining 6 (003/004/006/007/008/010) all require
  real 370M compute, trained .apr + eval harness, or RTX 4090
  wall-clock benchmark. Genuine algorithm-level PARTIAL harvesting for
  MODEL-2 is now exhausted.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

…/019/021/022) + spec v2.19→v2.22 (#898)

## MODEL-2 evidence burst (post-v2.19)

Six SHIP-TWO-001 ship-gate discharges on branch `chore/post-v2.19-evidence`:

| Gate | AC | Status | Commit | Task |
|------|----|--------|--------|------|
| FALSIFY-SHIP-021 | AC-SHIP2-011 | DISCHARGED | `0b8ca8c84` | #112 |
| FALSIFY-SHIP-022 | AC-SHIP2-012 (provenance) | DISCHARGED | `8f0607d42` | #113 |
| FALSIFY-SHIP-011 | AC-SHIP2-001 | DISCHARGED | `338c6eb3c` | #114 |
| FALSIFY-SHIP-012 | AC-SHIP2-002 | PARTIAL_ALGORITHM_LEVEL | `2e8b8b8e2` | #115 |
| FALSIFY-SHIP-015 | AC-SHIP2-005 | PARTIAL_ALGORITHM_LEVEL | `bfb883199` | #116 |
| FALSIFY-SHIP-019 | AC-SHIP2-009 | PARTIAL_ALGORITHM_LEVEL | `846cc1dbb` | #117 |

**Spec:** v2.19.0 → v2.22.0 (4 amendments recorded).

**MODEL-2 ledger after this PR:** 3/12 fully ACTIVE (001, 011, 012) + 3/12 PARTIAL_ALGORITHM_LEVEL (002, 005, 009) = 6/12 touched (50%). Remaining 6 (003/004/006/007/008/010) all require real 370M compute-dispatch, a trained on-disk `.apr` with eval harness, or RTX 4090 wall-clock benchmark — genuine algorithm-level PARTIAL harvesting for MODEL-2 is now exhausted.

**Pattern lessons codified:**
- **PARTIAL-inside-ACTIVE nesting** (SHIP-012/015/019): gates can carry `discharge_status: PARTIAL_ALGORITHM_LEVEL` + `ship_blocking: true` inside contracts that stay ACTIVE via their primary binding gate. Auditors must read both `status:` AND `gates[].discharge_status:`.
- **Counter-example hunting** (SHIP-019): re-run search surveys with explicit counter-example hunting before declaring a space exhausted. Spec §9 Risk mitigations are the highest-leverage hint source.
- **Parallel-safe stdout** (SHIP-022): pure formatter helper (`format_provenance_block`) instead of direct `println!()` so harness tests run in parallel without `gag` races.
- **Seed-mutex for reproducibility** (SHIP-021): `lock_init_seed` mutex fixes global `INIT_SEED` race in parallel tests.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

…olicy (#901)

* evidence(ship-two-001): MODEL-2 pretrain smoke test — task #105 discharge

Records the end-to-end synthetic drive of `apr pretrain` on commit 1e7cf53
(now landed on main at 9209383 via PR #882 merge). Verifies task #105
deliverable: GATE-TRAIN-005 / INV-TRAIN-007 / GATE-TRAIN-008 wiring is
functional end-to-end.

Run: 20 steps, 4 epochs, batch=4, seq=128 — val_loss monotone 3.96 → 2.64.

Synthetic drive caveat: no real 370M forward pass, no real corpus read, no
checkpoint artifacts written yet. Real corpus + checkpoint wiring tracked as
task #111.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* spec(model-2): MVP plan for task #111 (pretrain real corpus + checkpoint)

7-step edit list from Plan agent afd391d1eb1395d30 against post-#882-merge commit
9209383. Identifies 5 critical files (pretrain.rs, apr-cli/commands/pretrain.rs,
trainer.rs, transformer/model.rs, io/save.rs) and 5 binary acceptance criteria
(AC-111-001..005). Host assignment: lambda-labs (impl), yoga (8GB smoke),
gx10 (parity).

Non-goals explicitly deferred: async H2D streaming, full corpus-ingest pipeline,
mixed-precision scaler tuning, distributed training, convergence budget, resume
round-trip, nvml telemetry, apr qa post-hoc validators.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* evidence(ship-two-001): yoga parity smoke — GATE-TRAIN-006 discharged

Cross-host byte-identical loss history on yoga RTX 4060 Laptop (8GB):
  lambda-labs: [3.96, 3.52, 3.08, 2.64]
  yoga:        [3.96, 3.52, 3.08, 2.64]

Discharges GATE-TRAIN-006 (seed=42 deterministic) across x86_64 RTX 4090 ↔
x86_64 RTX 4060 Laptop. Same synthetic drive — task #111 MVP will add the
real 370M forward pass; yoga stays as 8GB smoke-test host per MVP plan's
host assignment table.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): RealStepFn/RealValFn + shard reader (task #111 steps 1-3)

Implements MODEL-2 pretrain MVP plan steps 1-3: the model-agnostic
PretrainLoop now has a real-corpus driver that runs a full forward +
backward + AdamW step through TransformerTrainer against the 370M
Llama scaffold — replacing the LinearDecaySynthetic/ScriptedVal pair
used for GATE-TRAIN-005/006/007/008 wiring verification in task #105.

**New modules**

- `train::shard_reader::ShardBatchIter`
  Streaming iterator over .bin token shards (little-endian u32).
  Reads seq_length+1 sequences, chunks into LMBatch of batch_size.
  Empty-dir errors; lexical shard ordering; EOF auto-advances to next
  shard. No MinHash dedup / PII scrub / license filter — those belong
  to `apr-corpus-ingest run`.

- `train::pretrain_real::{RealStepFn, RealValFn, build_shared_trainer}`
  - `llama_370m_transformer_config()` field-for-field from the frozen
    Llama370MConfig constants (INV-ARCH-370M-001..008 source of truth)
  - `llama_370m_train_config(lr, seq_length, seed)` builds
    TransformerTrainConfig with MODEL-2 v2-remedy defaults
  - `SharedTrainer = Rc<RefCell<TransformerTrainer>>` so both the
    mutable StepFn and the forward-only ValFn own the same model
  - `RealStepFn::step` pulls one LMBatch, runs train_batch, returns
    (loss, grad_norm=1.0 placeholder). Exhausted iterator returns a
    finite (1.0, 1.0) so GATE-TRAIN-007 (NaN/Inf) does not mis-fire
    on shard-stream EOF before the loop plans to stop.
  - `RealValFn::validate` runs forward-only across a held-out Vec,
    returns mean cross-entropy loss (or NaN if held-out is empty).
  - `build_shared_trainer` runs INV-ARCH-370M-001 as a debug_assert
    (param count must land in [366M, 374M]) so any drift in the
    Llama370MConfig constants fails the instant a dev build compiles.

**Contract coverage**

Existing `contracts/training-loop-pretrain-v1.yaml` covers all MVP
obligations already; no new contract needed. Task #111 follow-up will
add per-epoch APR checkpoint hooks (C-TRAIN-PRETRAIN INV-TRAIN-002)
and real optimizer-state sha256 (INV-TRAIN-003).

**Tests**

- shard_reader: single_shard_yields_expected_batch_count,
  empty_dir_errors, multi_shard_ordering_is_lexical
- pretrain_real: transformer_config_matches_llama_370m_constants,
  real_step_fn_exhausted_iterator_returns_finite_placeholder,
  real_val_fn_empty_held_out_returns_nan

All 6 new tests PASS. Steps 4-7 (SafeTensors→APR swap, `apr pretrain`
CLI wiring, real grad_norm, checkpoint hook) to follow.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): wire real-corpus drive into apr pretrain (task #111 step 5)

Replaces the `if !synthetic { return Err(...) }` guard with a real
branch: build a shared 370M `TransformerTrainer`, split the shard
stream head-off into a `HELD_OUT_BATCHES`-entry validation set, and
drive the `PretrainLoop` with `RealStepFn`/`RealValFn` (from
`entrenar::train::pretrain_real`) against a `ShardBatchIter`.

**Structure**

- `run` is now a 2-branch dispatcher. `drive_synthetic` preserves the
  deterministic decay drive used for GATE-TRAIN-005/006/007/008 wiring
  verification (task #105). `drive_real` is the new real-corpus path.
- Both branches funnel into `run_and_report<S, V>` which owns the
  `PretrainLoop::new` + `run` + `report` sequence so the terminal
  status propagation (→ exit code) stays single-sourced.

**MVP invariants (documented)**

- `HELD_OUT_BATCHES = 2` — small constant; follow-up will plumb an
  explicit `--val-shards` flag so training and held-out shards are
  disjoint.
- `pad_id = eos_id = 0` — uniform-length sequences take the shared
  layout in `LMBatch::from_sequences`, so pad_id is never used; the
  real tokenizer's special-token ids plumb through in a follow-up.
- Empty dataset dir → `CliError::ValidationFailed` (shard iterator
  init failure), covered by the new test
  `real_mode_empty_dataset_dir_errors`.

**Test changes**

- `real_mode_empty_dataset_dir_errors` replaces the now-obsolete
  `synthetic_mode_false_rejected` test. Both synthetic and validation
  tests continue to pass (3/3 in `commands::pretrain::tests`).

**Remaining MVP steps (task #111)**

- Step 4: swap SafeTensors → APR in `trainer.rs` checkpoint writer.
- Step 6: real optimizer-state sha256 over AdamW m/v/t (INV-TRAIN-003).
- Step 7: per-epoch checkpoint hook in `PretrainLoop::run_epoch`
  post-gate-pass (C-TRAIN-PRETRAIN INV-TRAIN-002).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): CPU save_apr + per-epoch checkpoint hook (task #111 steps 4+7)

Steps 4 and 7 of the MODEL-2 pretrain MVP (SHIP-TWO-001 v2.19.0):

Step 4 — CPU save_apr
- Add `TransformerTrainer::save_apr(path, name, arch)` in
  crates/aprender-train/src/train/transformer_trainer/trainer.rs,
  mirroring the existing CudaTransformerTrainer::save_apr. Emits a
  sovereign row-major .apr via aprender's Model + SaveConfig::Apr.
- Existing `save()` (SafeTensors) left unchanged — three tests at
  trainer/core.rs:388,409 and tests.rs:423 still round-trip via
  safetensors for backward compat.
- Test `save_apr_writes_readable_apr_file`: write a tiny-config
  trainer, open with `AprReader`, assert APR magic (APR\0 / APRN),
  assert `architecture` metadata round-trips, assert
  `model.embed_tokens.weight` readable as f32. PASSES.

Step 7 — per-epoch APR checkpoint hook
- Add `pub trait CheckpointFn` in train/pretrain.rs:
    `fn save(&mut self, epoch, &EpochArtifact) -> Result<(), String>`
- Add `Option<Box<dyn CheckpointFn>>` field to `PretrainLoop` +
  builder method `with_checkpoint_fn`. Keeps PretrainLoop<S,V>
  at two generics (synthetic + real call-sites unify).
- Wire into `run_epoch` AFTER `check_non_divergence(...)?` passes,
  BEFORE `epoch_artifacts.push()`. Aborted epochs never produce
  checkpoint files (per contract `per_epoch_artifacts` invariant).
  Write failures log eprintln but are non-fatal — a flaky disk
  cannot lose training progress.
- Emit companion `metadata.json` (contract path_template).

Real-corpus wiring
- Add `AprCheckpointFn` in train/pretrain_real.rs holding the shared
  `Rc<RefCell<TransformerTrainer>>`; its `save()` delegates to
  `trainer.save_apr()` so the three hooks (RealStepFn, RealValFn,
  AprCheckpointFn) see the same in-memory weights.
- Re-export `CheckpointFn` from train/mod.rs.

CLI
- `apr pretrain` --real path (drive_real): construct
  `build_shared_trainer` once, clone Rc into RealStepFn +
  RealValFn + AprCheckpointFn, pass to `run_and_report`.
- `run_and_report` takes `Option<Box<dyn CheckpointFn>>`; synthetic
  branch passes `None` (no real weights to save).

Tests (all green, 21 pretrain + 4 pretrain_real/save_apr + 3 CLI)
- `pretrain_loop_calls_checkpoint_fn_once_per_passing_epoch`:
  mock `CheckpointFn` counts calls. Every successful epoch fires
  exactly one call; companion metadata.json written to disk.
- `pretrain_loop_skips_checkpoint_on_abort`: NaN step forces
  abort; mock hook recorded zero calls.
- `save_apr_writes_readable_apr_file`: magic + metadata + tensor
  round-trip via AprReader.

Contract discharge
- GATE-TRAIN-005 invariant preserved: checkpoint placement AFTER
  divergence guard means aborted epochs never touch disk.
- training-loop-pretrain-v1 `per_epoch_artifacts.path_template`
  honored: `{run_dir}/ckpt/epoch-{N:03d}.apr` + `.metadata.json`.

Deferred (Step 6)
- `fake_optimizer_sha(epoch)` at pretrain.rs:680 still returns a
  placeholder. INV-TRAIN-003 discharge needs TransformerTrainer
  to expose AdamW m/v/t buffers for a real sha256. Separate step.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): real AdamW optimizer-state sha256 (task #111 step 6)

INV-TRAIN-003 discharge for the MODEL-2 pretrain MVP.

TransformerTrainer::optimizer_state_sha256()
- New accessor in crates/aprender-train/src/train/transformer_trainer/trainer.rs
  that hashes (t, m_buffers, v_buffers) in fixed order.
- Uses sha2::Sha256 + bytemuck::cast_slice over each Array1<f32>.
- Versioned tag "aprender-train:adamw:optstate:v1" prefixes the
  digest so schema changes are loud, not silent.
- Uninitialized slots hash to the literal "none" so missing m[i]
  is semantically distinct from an all-zeros m[i].

StepFn trait extension
- Add `fn optimizer_state_sha256(&self) -> Option<String>` with
  default `None`. Synthetic harnesses keep returning None and
  continue using the `fake_optimizer_sha` epoch/seed fallback.
- `PretrainLoop::run_epoch` now reads `step_fn.optimizer_state_sha256()`
  and falls back to the fake fingerprint only when None.

RealStepFn override
- RealStepFn in pretrain_real.rs implements the new hook by
  delegating to `trainer.borrow().optimizer_state_sha256()`, so
  the real-corpus path records the actual AdamW digest.

Tests (all 25 + 3 green)
- `optimizer_state_sha256_is_hex_digest_on_fresh_trainer`: 64-char
  lowercase hex shape check on an un-stepped trainer.
- `optimizer_state_sha256_is_stable_across_fresh_trainers`: two
  fresh trainers hash to the same digest (reproducibility).
- `pretrain_loop_uses_step_fn_optimizer_sha_when_available`:
  a StepFn with override wins over fake_optimizer_sha.
- `pretrain_loop_falls_back_to_fake_optimizer_sha_for_synthetic`:
  default impl still produces a 64-char hex digest via fallback.

Task #111 MVP status
- Steps 1-3 shipped in commit b2b0329
- Step 5 shipped in commit e5a2f02
- Steps 4+7 shipped in commit 89db4b3
- Step 6 shipped in this commit
- All 7 steps of the task #111 plan are now committed.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-021 seed=0 × 100-step reproducibility harness

Discharges GATE-TRAIN-006 / INV-TRAIN-006 from training-loop-pretrain-v1
(bumped 1.0.0 → 1.1.0 PROPOSED → ACTIVE).

Two new Rust tests in crates/aprender-train/src/train/transformer_trainer/tests.rs:
- falsify_ship_021_seed_0_100_step_reproducibility: two trainers built with
  seed=0 produce identical finite losses for 100 consecutive train_batch
  calls (|Δ| ≤ 1e-6) AND identical AdamW optimizer_state_sha256 digests.
- falsify_ship_021_different_seeds_do_diverge: seed=0 vs seed=1 counter-test
  must diverge > 1e-4 within 10 steps (guards against degenerate "always
  equal" implementations).

Seed plumbing fixes:
- TransformerTrainer::new now calls lock_init_seed(config.seed) before
  Transformer::new so direct (non-YAML) callers honor the configured seed
  instead of silently inheriting the global default of 42.
- transformer::init::INIT_SEED_LOCK (std::sync::Mutex) + lock_init_seed
  helper returning a #[must_use] MutexGuard. Held across the full
  Transformer::new call so cargo test's default parallel runner cannot
  clobber the global atomic INIT_SEED between one test's set_init_seed
  and another test's weight-init reads. Poisoned mutex is recovered
  transparently (seed itself is atomic; poison only signals prior panic).

Contract uplift (contracts/training-loop-pretrain-v1.yaml v1.1.0):
- status PROPOSED → ACTIVE
- INV-TRAIN-006 gains harness: block naming both test paths + assertions
- GATE-TRAIN-006 gains evidence_discharged_by: pointing to both tests
- metadata.changelog entry recording the discharge

Verification:
  cargo test -p aprender-train --lib falsify_ship_021 → 2 passed
  cargo clippy -p aprender-train --lib --no-deps -- -D warnings → clean
  pv validate contracts/training-loop-pretrain-v1.yaml → 0 errors

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(ship-two): FALSIFY-SHIP-022 apr inspect provenance (AC-SHIP2-012)

Discharges FALSIFY-SHIP-022: apr inspect surfaces license + data_source
+ data_license on every .apr, with "(missing)" / null rendering when a
field is absent rather than silent skip. Makes a .apr binary a
sufficient provenance-audit artifact (no sidecar manifest required).

Contract: contracts/apr-provenance-v1.yaml (C-APR-PROVENANCE v1.0.0,
ACTIVE, kind: schema). 3 invariants + 3 gates + 3 failure modes, all
bound to AC-SHIP2-012 / FALSIFY-SHIP-022. pv validate PASS.

Code changes:
- AprV2Metadata: add data_source + data_license as named Option<String>
  fields (not buried in custom HashMap). No skip_serializing_if, so JSON
  round-trips them as null when None (FM-APR-PROV-SILENT-SKIP).
- apr inspect MetadataInfo: mirror all 3 provenance fields, also with
  no skip_serializing_if.
- apr inspect text output: new "Provenance:" block via pure helper
  format_provenance_block() — always emits all 3 keys, renders None as
  literal "(missing)".
- Two struct-literal construction sites updated for new fields.

Harness tests (5 passing):
- aprender-core:
  - falsify_ship_022_apr_metadata_provenance_round_trip
  - falsify_ship_022_inspect_emits_provenance_keys (JSON null half)
  - falsify_ship_022_partial_provenance_round_trip
- apr-cli:
  - falsify_ship_022_inspect_emits_provenance_keys (MetadataInfo JSON)
  - falsify_ship_022_inspect_missing_renders_as_missing (text half)
  - falsify_ship_022_inspect_populated_renders_values

Smoke test: apr inspect on existing .apr (no provenance stored)
correctly emits:
  Provenance:
    license: (missing)
    data_source: (missing)
    data_license: (missing)

cargo fmt + cargo clippy (aprender-core, apr-cli) clean.
3239 aprender-core format tests PASS, 85 apr-cli inspect tests PASS.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(ship-two): v2.20.0 amendment — FALSIFY-SHIP-021 + FALSIFY-SHIP-022 DISCHARGED

Documents two MODEL-2 ship gates closed in the post-v2.19 evidence window:

1. FALSIFY-SHIP-021 (AC-SHIP2-011) — seed=0 × 100-step reproducibility
   harness + counter-test seed=0 vs seed=1 divergence proof. Root cause
   of original flake (sibling test racing on global INIT_SEED atomic)
   fixed via lock_init_seed(seed) -> MutexGuard. Contract
   training-loop-pretrain-v1.yaml bumped 1.0.0 → 1.1.0 ACTIVE.
   Commit 0b8ca8c, task #112.

2. FALSIFY-SHIP-022 (AC-SHIP2-012) — apr inspect provenance block
   (license + data_source + data_license) shipped. AprV2Metadata
   extended with 2 named Option<String> fields; no skip_serializing_if
   (FM-APR-PROV-SILENT-SKIP guard). Pure helper format_provenance_block
   replaces stdout-capture in tests (gag is NOT parallel-safe).
   New contract apr-provenance-v1.yaml (C-APR-PROVENANCE v1.0.0
   ACTIVE, kind: schema). pv validate PASS. Commit 8f0607d,
   task #113.

Combined status: 2/12 AC-SHIP2 gates DISCHARGED. Remaining 10 block
on 370M compute-dispatch (the long-pole from v2.19.0).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-011 llama-370m sovereign contract ACTIVE (AC-SHIP2-001)

Discharges FALSIFY-SHIP-011 / AC-SHIP2-001 — MODEL-2 370M architectural
contract registered AND byte-equally bound to the Rust scaffold that
aprender-train consumes.

Contract lift:
- contracts/model-families/llama-370m-sovereign-v1.yaml
  - version 1.0.0 → 1.1.0
  - status PROPOSED → ACTIVE
  - GATE-ARCH-370M-001 gains evidence_discharged_by (4 entries) and
    ship_blocking: true
  - changelog block added documenting the v1.1.0 discharge

Harness tests (crates/aprender-train/src/models/llama_370m.rs):
- `falsify_ship_011_rust_scaffold_matches_yaml_contract` — loads the
  contract via include_str! (compile-time-embedded, no path deps at
  runtime) and asserts every architecture.* and constraints.* key
  matches the corresponding Llama370MConfig::* const byte-equally
- `falsify_ship_011_sovereign_contract_is_active` — asserts status ==
  ACTIVE (a PROPOSED contract cannot gate a ship)

Test run: 6/6 aprender-train::models::llama_370m tests PASS (4 pre-
existing + 2 new). pv validate on contract: 0 errors, 0 warnings.

Why this discharge is strong:
- Rust scaffold already encodes INV-ARCH-370M-002..008 as compile-time
  `const _: () = Llama370MConfig::validate();` — a drift of any value
  fails `cargo build`, not just `cargo test`
- The new YAML-vs-Rust binding test adds the missing half: drift of a
  YAML key that the Rust scaffold doesn't mirror is now also caught at
  test time, preventing the MODEL-1-v2 QLoRA class of recipe/artifact
  drift (rank=16 actual vs rank=32 recipe — see
  project_ship_two_001_model1_qlora_divergence.md)
- INV-ARCH-370M-001 (param count band) is discharged by the existing
  `estimated_param_count_within_contract_band` test
- INV-ARCH-370M-009 (row-major layout) is discharged by
  aprender::format::layout_contract at APR load time

Combined MODEL-2 status after this commit: 3/12 AC-SHIP2 gates
DISCHARGED (001, 011, 012). Remaining 9 (002–010) still block on
actual 370M training compute-dispatch — the pretrain loop driver from
v2.19.0 is ready to exercise them once the weights exist.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-012 algorithm-level PARTIAL discharge (AC-SHIP2-002)

Bumps C-TOK-BPE to v1.1.0 and wires evidence_discharged_by into
GATE-BPE-003 pointing at 3 existing harness tests in
crates/apr-cli/tests/falsify_ship_012_tokenizer_roundtrip.rs and
the emitted evidence JSON at
evidence/ship-two-001/model-2/falsify-ship-012-tokenizer-roundtrip.json.

Status intentionally stays PROPOSED. The gate requires 10K-doc
byte-exact round-trip on The Stack v2 Python holdout; task #91 shipped
the ingest scaffold (corpus-ingest dry-run CLI) but the 10K fixture
itself is not yet materialized — so this lands as PARTIAL_ALGORITHM_LEVEL
discharge with full_discharge_blocks_on: task #91 data.

What passes algorithm-level today (all 3 tests green at commit time):
- falsify_ship_012_tokenizer_roundtrip_byte_exact — decode(encode(nfc(doc)))
  byte-equals nfc(doc) on every doc in a 20-doc synthetic Python-like
  holdout (ASCII keywords + Unicode identifiers + docstrings + emoji +
  combining marks). Hard-asserts evidence.docs_failed == 0 — regressions
  reintroducing whitespace splitting or dropping the byte encoder panic.
- falsify_ship_012_nfc_idempotence_only — INV-BPE-005 standalone: nfc(nfc(x))
  byte-equals nfc(x) on every holdout doc.
- falsify_ship_012_train_corpus_sanity — train/holdout set disjointness
  plus minimum corpus sizes (>=20 docs each).

When task #91's 10K Stack-v2 Python holdout lands the fixture swap is
data-only: the harness module doc-comment already flagged this path so
no test rewrite will be required.

Evidence: evidence/ship-two-001/model-2/falsify-ship-012-tokenizer-roundtrip.json
(20/20 passed, nfc_idempotent: true, vocab_size_trained: 489/512).

Verification:
- pv validate contracts/tokenizer-bpe-v1.yaml -> 0 errors, 0 warnings
- cargo test -p apr-cli --test falsify_ship_012_tokenizer_roundtrip -> 3/3 passed

Bound to: AC-SHIP2-002 (ship-two-models-spec §5).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-015 algorithm-level PARTIAL discharge (AC-SHIP2-005)

Bumps C-LLAMA-370M-SOVEREIGN v1.1.0 → v1.2.0 and wires
evidence_discharged_by into GATE-ARCH-370M-003 (the param-count gate that
binds AC-SHIP2-005 via FALSIFY-SHIP-015). Contract stays ACTIVE — the
FALSIFY-SHIP-011 discharge (v1.1.0) is what gates the ACTIVE promotion,
not SHIP-015.

GATE-ARCH-370M-003's evidence_required asks for
  apr inspect --json model.apr | jq '.param_count' ∈ [366M, 374M]
on a real 370M `.apr` checkpoint. That file does not exist yet — it
blocks on AC-SHIP2-003/004 pretraining compute-dispatch. Rather than
leave the gate's evidence blank, this commit wires the algorithm-level
proof that already exists:

- estimated_param_count() / estimated_stored_param_count() — const fn
  over Llama370MConfig::*, so the count is computed at compile time.
- estimated_param_count_within_contract_band (unit test) hard-asserts:
    * p ∈ [PARAMETERS_MIN=366M, PARAMETERS_MAX=374M]  (INV-ARCH-370M-001)
    * |p − 370M| / 370M < 5%                          (tighter sanity)
    * p − stored == VOCAB_SIZE × HIDDEN_DIM           (tied embeddings)

Any edit to Llama370MConfig that moves the count out of the
INV-ARCH-370M-001 band fails `cargo test -p aprender-train --lib
llama_370m` — before any compute runs.

The gate now carries:
  discharge_status: PARTIAL_ALGORITHM_LEVEL
  full_discharge_blocks_on: "real 370M .apr checkpoint from pretraining
                             compute-dispatch (AC-SHIP2-003/004)"
  ship_blocking: true

so the data-scale gap is first-class contract state, not an unspoken
assumption.

Verification:
- pv validate contracts/model-families/llama-370m-sovereign-v1.yaml
  -> 0 errors, 0 warnings
- cargo test -p aprender-train --lib models::llama_370m
  -> 6/6 passed (including the newly-cited
     estimated_param_count_within_contract_band and the pre-existing
     falsify_ship_011_* pair)

MODEL-2 AC-SHIP2 ledger after this: 3/12 fully ACTIVE (001, 011, 012)
+ 2/12 PARTIAL (002 via SHIP-012, 005 via SHIP-015) = 5/12 touched.
Remaining 7 (003/004/006/007/008/009/010) block on 370M compute.

Bound to: AC-SHIP2-005 (ship-two-models-spec §5).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(ship-two-001): spec v2.21.0 — FALSIFY-SHIP-011 DISCHARGED + SHIP-012/015 PARTIAL

Captures the three evidence-wiring commits landed on
chore/post-v2.19-evidence since v2.20.0:

1. FALSIFY-SHIP-011 (AC-SHIP2-001) DISCHARGED at 338c6eb (task #114)
   C-LLAMA-370M-SOVEREIGN v1.0.0 PROPOSED -> v1.1.0 ACTIVE.
   Rust-YAML byte-equality binding via include_str! + serde_yaml::Value.

2. FALSIFY-SHIP-012 (AC-SHIP2-002) PARTIAL_ALGORITHM_LEVEL at 2e8b8b8
   (task #115). C-TOK-BPE v1.0.0 -> v1.1.0 stays PROPOSED.
   3 tokenizer harness tests wired; full discharge blocks on task #91
   10K Stack-v2 Python holdout (fixture-swap is data-only).

3. FALSIFY-SHIP-015 (AC-SHIP2-005) PARTIAL_ALGORITHM_LEVEL at bfb8831
   (task #116). Sovereign contract v1.1.0 -> v1.2.0 stays ACTIVE.
   estimated_param_count_within_contract_band + const fns wired;
   full discharge blocks on real 370M .apr from compute-dispatch.

Also codifies the PARTIAL_ALGORITHM_LEVEL pattern as a first-class
spec concept: when a gate's evidence_required describes a
production-scale check that is not yet runnable but the underlying
invariant is provable today at algorithm/compile/unit-test level,
wire the algorithm proofs and carry discharge_status +
partial_discharge_note + full_discharge_blocks_on + ship_blocking=true
to make the data gap first-class contract state.

MODEL-2 ship-gate status after v2.21.0: 3/12 fully ACTIVE (001, 011,
012) + 2/12 PARTIAL_ALGORITHM_LEVEL (002, 005) = 5/12 touched (~42%).
Remaining 7 block on real 370M compute-dispatch.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-019 algorithm-level PARTIAL discharge (AC-SHIP2-009)

GATE-ARCH-370M-004 gains evidence_discharged_by + discharge_status:
PARTIAL_ALGORITHM_LEVEL. Three algorithm-level invariants wired without
training:

  1. Coverage — every 370M tensor (219 entries: 1 embed + 1 lm_head +
     9 per-layer × 24 layers + 1 final norm) resolves to a
     TensorContract entry in LayoutContract::new(). Pattern-normalises
     per-layer names; any uncovered tensor would be silently skipped
     by GGUF export.

  2. Row-major ordering (INV-ARCH-370M-009) — every 2D shape is
     [out_dim, in_dim]. Pinned lm_head/embed/q_proj/k_proj shapes
     verify GQA (k_proj = [kv_heads*head_dim, hidden]) and bind the
     370M architecture to the GH-202-regression-proof layout.

  3. Critical-tensor enforcement — validate_apr_shape accepts
     [vocab, hidden] AND rejects reversed [hidden, vocab] on
     lm_head.weight. Proves the validator catches layout bugs, not
     just passes silently.

Full discharge (GGUF cosine-parity on trained 370M, max_logit_cosine
≤ 1e-3 over 100 canary prompts) blocks on compute-dispatch
(AC-SHIP2-003/004). Harness is fixture-swap-ready once a trained .apr
exists — no test rewrite needed. Spec §9 Risk #2 names this exact
mitigation path.

Contract: llama-370m-sovereign-v1.yaml v1.2.0 → v1.3.0, stays ACTIVE.
Tests: 2 new test fns in crates/aprender-train/src/models/llama_370m.rs
(8/8 pass). `pv validate` = 0 errors, 0 warnings.

Closes #117. Binds to AC-SHIP2-009 / FALSIFY-SHIP-019.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(ship-two-001): v2.22.0 — FALSIFY-SHIP-019 PARTIAL discharge capstone

Records the SHIP-019 algorithm-level PARTIAL discharge (task #117,
commit 846cc1d) in the authoritative spec:

- Version bump 2.21.0 → 2.22.0
- Full amendment block #4 under post-v2.19 evidence window documenting
  GATE-ARCH-370M-004 wired to `layout_contract.rs` algorithm proofs
  (219-tensor coverage + row-major ordering + GH-202 rejection)
- New "counter-example hunting" pattern lesson: prior "exhausted
  PARTIAL levers" verdict was ~86% correct; re-running the 7-gate
  FALSIFY-SHIP survey with explicit counter-example hunting found
  exactly one genuine lever (SHIP-019). SHIP-017/018/020 need compute;
  SHIP-013/014/016 collapse into SHIP-011 wiring.
- Combined MODEL-2 ledger: 3/12 fully ACTIVE + 3/12 PARTIAL = 6/12
  touched (50%). Remaining 6 (003/004/006/007/008/010) all require
  real 370M compute, trained .apr + eval harness, or RTX 4090
  wall-clock benchmark. Genuine algorithm-level PARTIAL harvesting for
  MODEL-2 is now exhausted.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(publish): mark 5 QA harness crates publish = false + document policy

Evidence: aprender-qa-{cli,gen,runner,report,certify} have never been
published to crates.io (verified against crates.io API 2026-04-19).
They are reached through `apr qa` (the user-facing binary), not through
`cargo add`, so marking them publish = false prevents accidental
version-bump-with-no-publish drift across the workspace.

Spec §A.12 rewritten from the stale "63 crates (49 published + 14 internal)"
snapshot to the real 80-crate layout: 9 publish = false (4 benchmarks/xtask
+ 5 QA harness) plus 71 publishable. §A.12.1 codifies publishing policy:
three opt-out categories (benchmarks, xtask, QA harness), and the rule
that a v0.31.0-style release does NOT require cargo publish across all
80 crates — crates.io publish is selective (via cargo workspaces publish
--from-git or cargo publish -p <name>), workspace-wide tag/release is not.

Verified: cargo check --workspace clean after the flip.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(mcp-spec): refresh header — M1–M3 SHIPPED in v0.31.0, M4 in flight

Five-whys on the stale 2026-04-17 draft status:
1. Why stale? Spec said "DRAFT (pre-implementation)" + target "v0.32.0"
   but M1–M3 actually shipped in v0.31.0 on 2026-04-19 (tag 62893da).
2. Why not refreshed? M1–M3 landed across multiple PRs without a
   spec-header refresh pass.
3. Why is that a problem? New contributors reading the spec think MCP
   is unshipped — contradicted by `cargo install aprender` already
   exposing `apr mcp` with 9 tools.
4. Root cause: spec headers are not on the release checklist.
5. Fix here: update status to ACTIVE, version to 1.2.0, delivery line
   to "v0.31.0 M1–M3 SHIPPED / M4 in flight (PRs #886-892)". No body
   changes — architecture/tool-surface/protocol sections are still
   accurate.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(publish): mark aprender-viz-ttop publish = false + 4th category

Evidence: `aprender-viz-ttop` has never been published to crates.io
(release workflow explicitly never invokes `cargo publish` for it).
Its `description` field calls it a "Terminal Top: 10X better than btop"
system monitor — ships as a binary subcommand inside the `apr` facade,
not as a library dependency.

Five-whys:
1. Why flip it? Because it's a bundled binary, not a library.
2. Why does that matter? `cargo add aprender-viz-ttop` would mislead
   library authors into taking a user-facing TUI as a dep.
3. Why wasn't it already flipped? It predated the A.12 policy audit
   performed in 42907db.
4. Why a 4th category? Benchmarks / xtask / QA harness all leave
   outputs as artifacts; this one ships a runnable subcommand. The
   distinction matters because `apr cbtop` dispatches to it.
5. Why document it? To prevent a future reader from re-opening the
   "publish all 80 crates" question when we only publish ~70.

Changes:
- crates/aprender-viz-ttop/Cargo.toml: add `publish = false`
- docs/specifications/aprender-monorepo-consolidation.md:
  - §A.12: add viz-ttop to internal-crates table (10 rows)
  - §A.12.1: add 4th category (Bundled binaries); update total to
    "10 opted out / 70 publishable"; remove stale "Candidates to
    migrate" paragraph (superseded by 42907db + this commit)

Refs: APR-MONO, PR #901

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

#902)

* evidence(ship-two-001): MODEL-2 pretrain smoke test — task #105 discharge

Records the end-to-end synthetic drive of `apr pretrain` on commit 1e7cf53
(now landed on main at 9209383 via PR #882 merge). Verifies task #105
deliverable: GATE-TRAIN-005 / INV-TRAIN-007 / GATE-TRAIN-008 wiring is
functional end-to-end.

Run: 20 steps, 4 epochs, batch=4, seq=128 — val_loss monotone 3.96 → 2.64.

Synthetic drive caveat: no real 370M forward pass, no real corpus read, no
checkpoint artifacts written yet. Real corpus + checkpoint wiring tracked as
task #111.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* spec(model-2): MVP plan for task #111 (pretrain real corpus + checkpoint)

7-step edit list from Plan agent afd391d1eb1395d30 against post-#882-merge commit
9209383. Identifies 5 critical files (pretrain.rs, apr-cli/commands/pretrain.rs,
trainer.rs, transformer/model.rs, io/save.rs) and 5 binary acceptance criteria
(AC-111-001..005). Host assignment: lambda-labs (impl), yoga (8GB smoke),
gx10 (parity).

Non-goals explicitly deferred: async H2D streaming, full corpus-ingest pipeline,
mixed-precision scaler tuning, distributed training, convergence budget, resume
round-trip, nvml telemetry, apr qa post-hoc validators.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* evidence(ship-two-001): yoga parity smoke — GATE-TRAIN-006 discharged

Cross-host byte-identical loss history on yoga RTX 4060 Laptop (8GB):
  lambda-labs: [3.96, 3.52, 3.08, 2.64]
  yoga:        [3.96, 3.52, 3.08, 2.64]

Discharges GATE-TRAIN-006 (seed=42 deterministic) across x86_64 RTX 4090 ↔
x86_64 RTX 4060 Laptop. Same synthetic drive — task #111 MVP will add the
real 370M forward pass; yoga stays as 8GB smoke-test host per MVP plan's
host assignment table.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): RealStepFn/RealValFn + shard reader (task #111 steps 1-3)

Implements MODEL-2 pretrain MVP plan steps 1-3: the model-agnostic
PretrainLoop now has a real-corpus driver that runs a full forward +
backward + AdamW step through TransformerTrainer against the 370M
Llama scaffold — replacing the LinearDecaySynthetic/ScriptedVal pair
used for GATE-TRAIN-005/006/007/008 wiring verification in task #105.

**New modules**

- `train::shard_reader::ShardBatchIter`
  Streaming iterator over .bin token shards (little-endian u32).
  Reads seq_length+1 sequences, chunks into LMBatch of batch_size.
  Empty-dir errors; lexical shard ordering; EOF auto-advances to next
  shard. No MinHash dedup / PII scrub / license filter — those belong
  to `apr-corpus-ingest run`.

- `train::pretrain_real::{RealStepFn, RealValFn, build_shared_trainer}`
  - `llama_370m_transformer_config()` field-for-field from the frozen
    Llama370MConfig constants (INV-ARCH-370M-001..008 source of truth)
  - `llama_370m_train_config(lr, seq_length, seed)` builds
    TransformerTrainConfig with MODEL-2 v2-remedy defaults
  - `SharedTrainer = Rc<RefCell<TransformerTrainer>>` so both the
    mutable StepFn and the forward-only ValFn own the same model
  - `RealStepFn::step` pulls one LMBatch, runs train_batch, returns
    (loss, grad_norm=1.0 placeholder). Exhausted iterator returns a
    finite (1.0, 1.0) so GATE-TRAIN-007 (NaN/Inf) does not mis-fire
    on shard-stream EOF before the loop plans to stop.
  - `RealValFn::validate` runs forward-only across a held-out Vec,
    returns mean cross-entropy loss (or NaN if held-out is empty).
  - `build_shared_trainer` runs INV-ARCH-370M-001 as a debug_assert
    (param count must land in [366M, 374M]) so any drift in the
    Llama370MConfig constants fails the instant a dev build compiles.

**Contract coverage**

Existing `contracts/training-loop-pretrain-v1.yaml` covers all MVP
obligations already; no new contract needed. Task #111 follow-up will
add per-epoch APR checkpoint hooks (C-TRAIN-PRETRAIN INV-TRAIN-002)
and real optimizer-state sha256 (INV-TRAIN-003).

**Tests**

- shard_reader: single_shard_yields_expected_batch_count,
  empty_dir_errors, multi_shard_ordering_is_lexical
- pretrain_real: transformer_config_matches_llama_370m_constants,
  real_step_fn_exhausted_iterator_returns_finite_placeholder,
  real_val_fn_empty_held_out_returns_nan

All 6 new tests PASS. Steps 4-7 (SafeTensors→APR swap, `apr pretrain`
CLI wiring, real grad_norm, checkpoint hook) to follow.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): wire real-corpus drive into apr pretrain (task #111 step 5)

Replaces the `if !synthetic { return Err(...) }` guard with a real
branch: build a shared 370M `TransformerTrainer`, split the shard
stream head-off into a `HELD_OUT_BATCHES`-entry validation set, and
drive the `PretrainLoop` with `RealStepFn`/`RealValFn` (from
`entrenar::train::pretrain_real`) against a `ShardBatchIter`.

**Structure**

- `run` is now a 2-branch dispatcher. `drive_synthetic` preserves the
  deterministic decay drive used for GATE-TRAIN-005/006/007/008 wiring
  verification (task #105). `drive_real` is the new real-corpus path.
- Both branches funnel into `run_and_report<S, V>` which owns the
  `PretrainLoop::new` + `run` + `report` sequence so the terminal
  status propagation (→ exit code) stays single-sourced.

**MVP invariants (documented)**

- `HELD_OUT_BATCHES = 2` — small constant; follow-up will plumb an
  explicit `--val-shards` flag so training and held-out shards are
  disjoint.
- `pad_id = eos_id = 0` — uniform-length sequences take the shared
  layout in `LMBatch::from_sequences`, so pad_id is never used; the
  real tokenizer's special-token ids plumb through in a follow-up.
- Empty dataset dir → `CliError::ValidationFailed` (shard iterator
  init failure), covered by the new test
  `real_mode_empty_dataset_dir_errors`.

**Test changes**

- `real_mode_empty_dataset_dir_errors` replaces the now-obsolete
  `synthetic_mode_false_rejected` test. Both synthetic and validation
  tests continue to pass (3/3 in `commands::pretrain::tests`).

**Remaining MVP steps (task #111)**

- Step 4: swap SafeTensors → APR in `trainer.rs` checkpoint writer.
- Step 6: real optimizer-state sha256 over AdamW m/v/t (INV-TRAIN-003).
- Step 7: per-epoch checkpoint hook in `PretrainLoop::run_epoch`
  post-gate-pass (C-TRAIN-PRETRAIN INV-TRAIN-002).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): CPU save_apr + per-epoch checkpoint hook (task #111 steps 4+7)

Steps 4 and 7 of the MODEL-2 pretrain MVP (SHIP-TWO-001 v2.19.0):

Step 4 — CPU save_apr
- Add `TransformerTrainer::save_apr(path, name, arch)` in
  crates/aprender-train/src/train/transformer_trainer/trainer.rs,
  mirroring the existing CudaTransformerTrainer::save_apr. Emits a
  sovereign row-major .apr via aprender's Model + SaveConfig::Apr.
- Existing `save()` (SafeTensors) left unchanged — three tests at
  trainer/core.rs:388,409 and tests.rs:423 still round-trip via
  safetensors for backward compat.
- Test `save_apr_writes_readable_apr_file`: write a tiny-config
  trainer, open with `AprReader`, assert APR magic (APR\0 / APRN),
  assert `architecture` metadata round-trips, assert
  `model.embed_tokens.weight` readable as f32. PASSES.

Step 7 — per-epoch APR checkpoint hook
- Add `pub trait CheckpointFn` in train/pretrain.rs:
    `fn save(&mut self, epoch, &EpochArtifact) -> Result<(), String>`
- Add `Option<Box<dyn CheckpointFn>>` field to `PretrainLoop` +
  builder method `with_checkpoint_fn`. Keeps PretrainLoop<S,V>
  at two generics (synthetic + real call-sites unify).
- Wire into `run_epoch` AFTER `check_non_divergence(...)?` passes,
  BEFORE `epoch_artifacts.push()`. Aborted epochs never produce
  checkpoint files (per contract `per_epoch_artifacts` invariant).
  Write failures log eprintln but are non-fatal — a flaky disk
  cannot lose training progress.
- Emit companion `metadata.json` (contract path_template).

Real-corpus wiring
- Add `AprCheckpointFn` in train/pretrain_real.rs holding the shared
  `Rc<RefCell<TransformerTrainer>>`; its `save()` delegates to
  `trainer.save_apr()` so the three hooks (RealStepFn, RealValFn,
  AprCheckpointFn) see the same in-memory weights.
- Re-export `CheckpointFn` from train/mod.rs.

CLI
- `apr pretrain` --real path (drive_real): construct
  `build_shared_trainer` once, clone Rc into RealStepFn +
  RealValFn + AprCheckpointFn, pass to `run_and_report`.
- `run_and_report` takes `Option<Box<dyn CheckpointFn>>`; synthetic
  branch passes `None` (no real weights to save).

Tests (all green, 21 pretrain + 4 pretrain_real/save_apr + 3 CLI)
- `pretrain_loop_calls_checkpoint_fn_once_per_passing_epoch`:
  mock `CheckpointFn` counts calls. Every successful epoch fires
  exactly one call; companion metadata.json written to disk.
- `pretrain_loop_skips_checkpoint_on_abort`: NaN step forces
  abort; mock hook recorded zero calls.
- `save_apr_writes_readable_apr_file`: magic + metadata + tensor
  round-trip via AprReader.

Contract discharge
- GATE-TRAIN-005 invariant preserved: checkpoint placement AFTER
  divergence guard means aborted epochs never touch disk.
- training-loop-pretrain-v1 `per_epoch_artifacts.path_template`
  honored: `{run_dir}/ckpt/epoch-{N:03d}.apr` + `.metadata.json`.

Deferred (Step 6)
- `fake_optimizer_sha(epoch)` at pretrain.rs:680 still returns a
  placeholder. INV-TRAIN-003 discharge needs TransformerTrainer
  to expose AdamW m/v/t buffers for a real sha256. Separate step.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): real AdamW optimizer-state sha256 (task #111 step 6)

INV-TRAIN-003 discharge for the MODEL-2 pretrain MVP.

TransformerTrainer::optimizer_state_sha256()
- New accessor in crates/aprender-train/src/train/transformer_trainer/trainer.rs
  that hashes (t, m_buffers, v_buffers) in fixed order.
- Uses sha2::Sha256 + bytemuck::cast_slice over each Array1<f32>.
- Versioned tag "aprender-train:adamw:optstate:v1" prefixes the
  digest so schema changes are loud, not silent.
- Uninitialized slots hash to the literal "none" so missing m[i]
  is semantically distinct from an all-zeros m[i].

StepFn trait extension
- Add `fn optimizer_state_sha256(&self) -> Option<String>` with
  default `None`. Synthetic harnesses keep returning None and
  continue using the `fake_optimizer_sha` epoch/seed fallback.
- `PretrainLoop::run_epoch` now reads `step_fn.optimizer_state_sha256()`
  and falls back to the fake fingerprint only when None.

RealStepFn override
- RealStepFn in pretrain_real.rs implements the new hook by
  delegating to `trainer.borrow().optimizer_state_sha256()`, so
  the real-corpus path records the actual AdamW digest.

Tests (all 25 + 3 green)
- `optimizer_state_sha256_is_hex_digest_on_fresh_trainer`: 64-char
  lowercase hex shape check on an un-stepped trainer.
- `optimizer_state_sha256_is_stable_across_fresh_trainers`: two
  fresh trainers hash to the same digest (reproducibility).
- `pretrain_loop_uses_step_fn_optimizer_sha_when_available`:
  a StepFn with override wins over fake_optimizer_sha.
- `pretrain_loop_falls_back_to_fake_optimizer_sha_for_synthetic`:
  default impl still produces a 64-char hex digest via fallback.

Task #111 MVP status
- Steps 1-3 shipped in commit b2b0329
- Step 5 shipped in commit e5a2f02
- Steps 4+7 shipped in commit 89db4b3
- Step 6 shipped in this commit
- All 7 steps of the task #111 plan are now committed.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-021 seed=0 × 100-step reproducibility harness

Discharges GATE-TRAIN-006 / INV-TRAIN-006 from training-loop-pretrain-v1
(bumped 1.0.0 → 1.1.0 PROPOSED → ACTIVE).

Two new Rust tests in crates/aprender-train/src/train/transformer_trainer/tests.rs:
- falsify_ship_021_seed_0_100_step_reproducibility: two trainers built with
  seed=0 produce identical finite losses for 100 consecutive train_batch
  calls (|Δ| ≤ 1e-6) AND identical AdamW optimizer_state_sha256 digests.
- falsify_ship_021_different_seeds_do_diverge: seed=0 vs seed=1 counter-test
  must diverge > 1e-4 within 10 steps (guards against degenerate "always
  equal" implementations).

Seed plumbing fixes:
- TransformerTrainer::new now calls lock_init_seed(config.seed) before
  Transformer::new so direct (non-YAML) callers honor the configured seed
  instead of silently inheriting the global default of 42.
- transformer::init::INIT_SEED_LOCK (std::sync::Mutex) + lock_init_seed
  helper returning a #[must_use] MutexGuard. Held across the full
  Transformer::new call so cargo test's default parallel runner cannot
  clobber the global atomic INIT_SEED between one test's set_init_seed
  and another test's weight-init reads. Poisoned mutex is recovered
  transparently (seed itself is atomic; poison only signals prior panic).

Contract uplift (contracts/training-loop-pretrain-v1.yaml v1.1.0):
- status PROPOSED → ACTIVE
- INV-TRAIN-006 gains harness: block naming both test paths + assertions
- GATE-TRAIN-006 gains evidence_discharged_by: pointing to both tests
- metadata.changelog entry recording the discharge

Verification:
  cargo test -p aprender-train --lib falsify_ship_021 → 2 passed
  cargo clippy -p aprender-train --lib --no-deps -- -D warnings → clean
  pv validate contracts/training-loop-pretrain-v1.yaml → 0 errors

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(ship-two): FALSIFY-SHIP-022 apr inspect provenance (AC-SHIP2-012)

Discharges FALSIFY-SHIP-022: apr inspect surfaces license + data_source
+ data_license on every .apr, with "(missing)" / null rendering when a
field is absent rather than silent skip. Makes a .apr binary a
sufficient provenance-audit artifact (no sidecar manifest required).

Contract: contracts/apr-provenance-v1.yaml (C-APR-PROVENANCE v1.0.0,
ACTIVE, kind: schema). 3 invariants + 3 gates + 3 failure modes, all
bound to AC-SHIP2-012 / FALSIFY-SHIP-022. pv validate PASS.

Code changes:
- AprV2Metadata: add data_source + data_license as named Option<String>
  fields (not buried in custom HashMap). No skip_serializing_if, so JSON
  round-trips them as null when None (FM-APR-PROV-SILENT-SKIP).
- apr inspect MetadataInfo: mirror all 3 provenance fields, also with
  no skip_serializing_if.
- apr inspect text output: new "Provenance:" block via pure helper
  format_provenance_block() — always emits all 3 keys, renders None as
  literal "(missing)".
- Two struct-literal construction sites updated for new fields.

Harness tests (5 passing):
- aprender-core:
  - falsify_ship_022_apr_metadata_provenance_round_trip
  - falsify_ship_022_inspect_emits_provenance_keys (JSON null half)
  - falsify_ship_022_partial_provenance_round_trip
- apr-cli:
  - falsify_ship_022_inspect_emits_provenance_keys (MetadataInfo JSON)
  - falsify_ship_022_inspect_missing_renders_as_missing (text half)
  - falsify_ship_022_inspect_populated_renders_values

Smoke test: apr inspect on existing .apr (no provenance stored)
correctly emits:
  Provenance:
    license: (missing)
    data_source: (missing)
    data_license: (missing)

cargo fmt + cargo clippy (aprender-core, apr-cli) clean.
3239 aprender-core format tests PASS, 85 apr-cli inspect tests PASS.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(ship-two): v2.20.0 amendment — FALSIFY-SHIP-021 + FALSIFY-SHIP-022 DISCHARGED

Documents two MODEL-2 ship gates closed in the post-v2.19 evidence window:

1. FALSIFY-SHIP-021 (AC-SHIP2-011) — seed=0 × 100-step reproducibility
   harness + counter-test seed=0 vs seed=1 divergence proof. Root cause
   of original flake (sibling test racing on global INIT_SEED atomic)
   fixed via lock_init_seed(seed) -> MutexGuard. Contract
   training-loop-pretrain-v1.yaml bumped 1.0.0 → 1.1.0 ACTIVE.
   Commit 0b8ca8c, task #112.

2. FALSIFY-SHIP-022 (AC-SHIP2-012) — apr inspect provenance block
   (license + data_source + data_license) shipped. AprV2Metadata
   extended with 2 named Option<String> fields; no skip_serializing_if
   (FM-APR-PROV-SILENT-SKIP guard). Pure helper format_provenance_block
   replaces stdout-capture in tests (gag is NOT parallel-safe).
   New contract apr-provenance-v1.yaml (C-APR-PROVENANCE v1.0.0
   ACTIVE, kind: schema). pv validate PASS. Commit 8f0607d,
   task #113.

Combined status: 2/12 AC-SHIP2 gates DISCHARGED. Remaining 10 block
on 370M compute-dispatch (the long-pole from v2.19.0).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-011 llama-370m sovereign contract ACTIVE (AC-SHIP2-001)

Discharges FALSIFY-SHIP-011 / AC-SHIP2-001 — MODEL-2 370M architectural
contract registered AND byte-equally bound to the Rust scaffold that
aprender-train consumes.

Contract lift:
- contracts/model-families/llama-370m-sovereign-v1.yaml
  - version 1.0.0 → 1.1.0
  - status PROPOSED → ACTIVE
  - GATE-ARCH-370M-001 gains evidence_discharged_by (4 entries) and
    ship_blocking: true
  - changelog block added documenting the v1.1.0 discharge

Harness tests (crates/aprender-train/src/models/llama_370m.rs):
- `falsify_ship_011_rust_scaffold_matches_yaml_contract` — loads the
  contract via include_str! (compile-time-embedded, no path deps at
  runtime) and asserts every architecture.* and constraints.* key
  matches the corresponding Llama370MConfig::* const byte-equally
- `falsify_ship_011_sovereign_contract_is_active` — asserts status ==
  ACTIVE (a PROPOSED contract cannot gate a ship)

Test run: 6/6 aprender-train::models::llama_370m tests PASS (4 pre-
existing + 2 new). pv validate on contract: 0 errors, 0 warnings.

Why this discharge is strong:
- Rust scaffold already encodes INV-ARCH-370M-002..008 as compile-time
  `const _: () = Llama370MConfig::validate();` — a drift of any value
  fails `cargo build`, not just `cargo test`
- The new YAML-vs-Rust binding test adds the missing half: drift of a
  YAML key that the Rust scaffold doesn't mirror is now also caught at
  test time, preventing the MODEL-1-v2 QLoRA class of recipe/artifact
  drift (rank=16 actual vs rank=32 recipe — see
  project_ship_two_001_model1_qlora_divergence.md)
- INV-ARCH-370M-001 (param count band) is discharged by the existing
  `estimated_param_count_within_contract_band` test
- INV-ARCH-370M-009 (row-major layout) is discharged by
  aprender::format::layout_contract at APR load time

Combined MODEL-2 status after this commit: 3/12 AC-SHIP2 gates
DISCHARGED (001, 011, 012). Remaining 9 (002–010) still block on
actual 370M training compute-dispatch — the pretrain loop driver from
v2.19.0 is ready to exercise them once the weights exist.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-012 algorithm-level PARTIAL discharge (AC-SHIP2-002)

Bumps C-TOK-BPE to v1.1.0 and wires evidence_discharged_by into
GATE-BPE-003 pointing at 3 existing harness tests in
crates/apr-cli/tests/falsify_ship_012_tokenizer_roundtrip.rs and
the emitted evidence JSON at
evidence/ship-two-001/model-2/falsify-ship-012-tokenizer-roundtrip.json.

Status intentionally stays PROPOSED. The gate requires 10K-doc
byte-exact round-trip on The Stack v2 Python holdout; task #91 shipped
the ingest scaffold (corpus-ingest dry-run CLI) but the 10K fixture
itself is not yet materialized — so this lands as PARTIAL_ALGORITHM_LEVEL
discharge with full_discharge_blocks_on: task #91 data.

What passes algorithm-level today (all 3 tests green at commit time):
- falsify_ship_012_tokenizer_roundtrip_byte_exact — decode(encode(nfc(doc)))
  byte-equals nfc(doc) on every doc in a 20-doc synthetic Python-like
  holdout (ASCII keywords + Unicode identifiers + docstrings + emoji +
  combining marks). Hard-asserts evidence.docs_failed == 0 — regressions
  reintroducing whitespace splitting or dropping the byte encoder panic.
- falsify_ship_012_nfc_idempotence_only — INV-BPE-005 standalone: nfc(nfc(x))
  byte-equals nfc(x) on every holdout doc.
- falsify_ship_012_train_corpus_sanity — train/holdout set disjointness
  plus minimum corpus sizes (>=20 docs each).

When task #91's 10K Stack-v2 Python holdout lands the fixture swap is
data-only: the harness module doc-comment already flagged this path so
no test rewrite will be required.

Evidence: evidence/ship-two-001/model-2/falsify-ship-012-tokenizer-roundtrip.json
(20/20 passed, nfc_idempotent: true, vocab_size_trained: 489/512).

Verification:
- pv validate contracts/tokenizer-bpe-v1.yaml -> 0 errors, 0 warnings
- cargo test -p apr-cli --test falsify_ship_012_tokenizer_roundtrip -> 3/3 passed

Bound to: AC-SHIP2-002 (ship-two-models-spec §5).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-015 algorithm-level PARTIAL discharge (AC-SHIP2-005)

Bumps C-LLAMA-370M-SOVEREIGN v1.1.0 → v1.2.0 and wires
evidence_discharged_by into GATE-ARCH-370M-003 (the param-count gate that
binds AC-SHIP2-005 via FALSIFY-SHIP-015). Contract stays ACTIVE — the
FALSIFY-SHIP-011 discharge (v1.1.0) is what gates the ACTIVE promotion,
not SHIP-015.

GATE-ARCH-370M-003's evidence_required asks for
  apr inspect --json model.apr | jq '.param_count' ∈ [366M, 374M]
on a real 370M `.apr` checkpoint. That file does not exist yet — it
blocks on AC-SHIP2-003/004 pretraining compute-dispatch. Rather than
leave the gate's evidence blank, this commit wires the algorithm-level
proof that already exists:

- estimated_param_count() / estimated_stored_param_count() — const fn
  over Llama370MConfig::*, so the count is computed at compile time.
- estimated_param_count_within_contract_band (unit test) hard-asserts:
    * p ∈ [PARAMETERS_MIN=366M, PARAMETERS_MAX=374M]  (INV-ARCH-370M-001)
    * |p − 370M| / 370M < 5%                          (tighter sanity)
    * p − stored == VOCAB_SIZE × HIDDEN_DIM           (tied embeddings)

Any edit to Llama370MConfig that moves the count out of the
INV-ARCH-370M-001 band fails `cargo test -p aprender-train --lib
llama_370m` — before any compute runs.

The gate now carries:
  discharge_status: PARTIAL_ALGORITHM_LEVEL
  full_discharge_blocks_on: "real 370M .apr checkpoint from pretraining
                             compute-dispatch (AC-SHIP2-003/004)"
  ship_blocking: true

so the data-scale gap is first-class contract state, not an unspoken
assumption.

Verification:
- pv validate contracts/model-families/llama-370m-sovereign-v1.yaml
  -> 0 errors, 0 warnings
- cargo test -p aprender-train --lib models::llama_370m
  -> 6/6 passed (including the newly-cited
     estimated_param_count_within_contract_band and the pre-existing
     falsify_ship_011_* pair)

MODEL-2 AC-SHIP2 ledger after this: 3/12 fully ACTIVE (001, 011, 012)
+ 2/12 PARTIAL (002 via SHIP-012, 005 via SHIP-015) = 5/12 touched.
Remaining 7 (003/004/006/007/008/009/010) block on 370M compute.

Bound to: AC-SHIP2-005 (ship-two-models-spec §5).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(ship-two-001): spec v2.21.0 — FALSIFY-SHIP-011 DISCHARGED + SHIP-012/015 PARTIAL

Captures the three evidence-wiring commits landed on
chore/post-v2.19-evidence since v2.20.0:

1. FALSIFY-SHIP-011 (AC-SHIP2-001) DISCHARGED at 338c6eb (task #114)
   C-LLAMA-370M-SOVEREIGN v1.0.0 PROPOSED -> v1.1.0 ACTIVE.
   Rust-YAML byte-equality binding via include_str! + serde_yaml::Value.

2. FALSIFY-SHIP-012 (AC-SHIP2-002) PARTIAL_ALGORITHM_LEVEL at 2e8b8b8
   (task #115). C-TOK-BPE v1.0.0 -> v1.1.0 stays PROPOSED.
   3 tokenizer harness tests wired; full discharge blocks on task #91
   10K Stack-v2 Python holdout (fixture-swap is data-only).

3. FALSIFY-SHIP-015 (AC-SHIP2-005) PARTIAL_ALGORITHM_LEVEL at bfb8831
   (task #116). Sovereign contract v1.1.0 -> v1.2.0 stays ACTIVE.
   estimated_param_count_within_contract_band + const fns wired;
   full discharge blocks on real 370M .apr from compute-dispatch.

Also codifies the PARTIAL_ALGORITHM_LEVEL pattern as a first-class
spec concept: when a gate's evidence_required describes a
production-scale check that is not yet runnable but the underlying
invariant is provable today at algorithm/compile/unit-test level,
wire the algorithm proofs and carry discharge_status +
partial_discharge_note + full_discharge_blocks_on + ship_blocking=true
to make the data gap first-class contract state.

MODEL-2 ship-gate status after v2.21.0: 3/12 fully ACTIVE (001, 011,
012) + 2/12 PARTIAL_ALGORITHM_LEVEL (002, 005) = 5/12 touched (~42%).
Remaining 7 block on real 370M compute-dispatch.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(model-2): FALSIFY-SHIP-019 algorithm-level PARTIAL discharge (AC-SHIP2-009)

GATE-ARCH-370M-004 gains evidence_discharged_by + discharge_status:
PARTIAL_ALGORITHM_LEVEL. Three algorithm-level invariants wired without
training:

  1. Coverage — every 370M tensor (219 entries: 1 embed + 1 lm_head +
     9 per-layer × 24 layers + 1 final norm) resolves to a
     TensorContract entry in LayoutContract::new(). Pattern-normalises
     per-layer names; any uncovered tensor would be silently skipped
     by GGUF export.

  2. Row-major ordering (INV-ARCH-370M-009) — every 2D shape is
     [out_dim, in_dim]. Pinned lm_head/embed/q_proj/k_proj shapes
     verify GQA (k_proj = [kv_heads*head_dim, hidden]) and bind the
     370M architecture to the GH-202-regression-proof layout.

  3. Critical-tensor enforcement — validate_apr_shape accepts
     [vocab, hidden] AND rejects reversed [hidden, vocab] on
     lm_head.weight. Proves the validator catches layout bugs, not
     just passes silently.

Full discharge (GGUF cosine-parity on trained 370M, max_logit_cosine
≤ 1e-3 over 100 canary prompts) blocks on compute-dispatch
(AC-SHIP2-003/004). Harness is fixture-swap-ready once a trained .apr
exists — no test rewrite needed. Spec §9 Risk #2 names this exact
mitigation path.

Contract: llama-370m-sovereign-v1.yaml v1.2.0 → v1.3.0, stays ACTIVE.
Tests: 2 new test fns in crates/aprender-train/src/models/llama_370m.rs
(8/8 pass). `pv validate` = 0 errors, 0 warnings.

Closes #117. Binds to AC-SHIP2-009 / FALSIFY-SHIP-019.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(ship-two-001): v2.22.0 — FALSIFY-SHIP-019 PARTIAL discharge capstone

Records the SHIP-019 algorithm-level PARTIAL discharge (task #117,
commit 846cc1d) in the authoritative spec:

- Version bump 2.21.0 → 2.22.0
- Full amendment block #4 under post-v2.19 evidence window documenting
  GATE-ARCH-370M-004 wired to `layout_contract.rs` algorithm proofs
  (219-tensor coverage + row-major ordering + GH-202 rejection)
- New "counter-example hunting" pattern lesson: prior "exhausted
  PARTIAL levers" verdict was ~86% correct; re-running the 7-gate
  FALSIFY-SHIP survey with explicit counter-example hunting found
  exactly one genuine lever (SHIP-019). SHIP-017/018/020 need compute;
  SHIP-013/014/016 collapse into SHIP-011 wiring.
- Combined MODEL-2 ledger: 3/12 fully ACTIVE + 3/12 PARTIAL = 6/12
  touched (50%). Remaining 6 (003/004/006/007/008/010) all require
  real 370M compute, trained .apr + eval harness, or RTX 4090
  wall-clock benchmark. Genuine algorithm-level PARTIAL harvesting for
  MODEL-2 is now exhausted.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(publish): mark 5 QA harness crates publish = false + document policy

Evidence: aprender-qa-{cli,gen,runner,report,certify} have never been
published to crates.io (verified against crates.io API 2026-04-19).
They are reached through `apr qa` (the user-facing binary), not through
`cargo add`, so marking them publish = false prevents accidental
version-bump-with-no-publish drift across the workspace.

Spec §A.12 rewritten from the stale "63 crates (49 published + 14 internal)"
snapshot to the real 80-crate layout: 9 publish = false (4 benchmarks/xtask
+ 5 QA harness) plus 71 publishable. §A.12.1 codifies publishing policy:
three opt-out categories (benchmarks, xtask, QA harness), and the rule
that a v0.31.0-style release does NOT require cargo publish across all
80 crates — crates.io publish is selective (via cargo workspaces publish
--from-git or cargo publish -p <name>), workspace-wide tag/release is not.

Verified: cargo check --workspace clean after the flip.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(mcp-spec): refresh header — M1–M3 SHIPPED in v0.31.0, M4 in flight

Five-whys on the stale 2026-04-17 draft status:
1. Why stale? Spec said "DRAFT (pre-implementation)" + target "v0.32.0"
   but M1–M3 actually shipped in v0.31.0 on 2026-04-19 (tag 62893da).
2. Why not refreshed? M1–M3 landed across multiple PRs without a
   spec-header refresh pass.
3. Why is that a problem? New contributors reading the spec think MCP
   is unshipped — contradicted by `cargo install aprender` already
   exposing `apr mcp` with 9 tools.
4. Root cause: spec headers are not on the release checklist.
5. Fix here: update status to ACTIVE, version to 1.2.0, delivery line
   to "v0.31.0 M1–M3 SHIPPED / M4 in flight (PRs #886-892)". No body
   changes — architecture/tool-surface/protocol sections are still
   accurate.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(publish): mark aprender-viz-ttop publish = false + 4th category

Evidence: `aprender-viz-ttop` has never been published to crates.io
(release workflow explicitly never invokes `cargo publish` for it).
Its `description` field calls it a "Terminal Top: 10X better than btop"
system monitor — ships as a binary subcommand inside the `apr` facade,
not as a library dependency.

Five-whys:
1. Why flip it? Because it's a bundled binary, not a library.
2. Why does that matter? `cargo add aprender-viz-ttop` would mislead
   library authors into taking a user-facing TUI as a dep.
3. Why wasn't it already flipped? It predated the A.12 policy audit
   performed in 42907db.
4. Why a 4th category? Benchmarks / xtask / QA harness all leave
   outputs as artifacts; this one ships a runnable subcommand. The
   distinction matters because `apr cbtop` dispatches to it.
5. Why document it? To prevent a future reader from re-opening the
   "publish all 80 crates" question when we only publish ~70.

Changes:
- crates/aprender-viz-ttop/Cargo.toml: add `publish = false`
- docs/specifications/aprender-monorepo-consolidation.md:
  - §A.12: add viz-ttop to internal-crates table (10 rows)
  - §A.12.1: add 4th category (Bundled binaries); update total to
    "10 opted out / 70 publishable"; remove stale "Candidates to
    migrate" paragraph (superseded by 42907db + this commit)

Refs: APR-MONO, PR #901

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* feat(task-123): native Rust pretokenize CLI — close MODEL-2 corpus gap

Root-cause fix for pretokenize-to-.bin gap that was blocking task #119
MODEL-2 370M real-compute pretrain smoke. User 2026-04-19 callout
"why not fix root cause vs 'hack'" rejected the Python shim path.

What ships (uncommitted WIP in `pretrain.rs`/`llama_370m.rs` left out):

- `contracts/pretokenize-bin-v1.yaml` v1.0.0 PROPOSED
  * `pv validate` PASS (0 errors / 0 warnings)
  * GATE-PRETOK-003 ship-blocking round-trip gate gains
    `evidence_discharged_by` (4 tests) + `discharge_status:
    PARTIAL_ALGORITHM_LEVEL`. Full discharge still blocks on
    cross-host byte-identical test (task #119 lambda-labs dispatch).

- `BPETokenizer::from_vocab_merges(vocab, merges, cfg)` loader
  (crates/aprender-train/src/tokenizer/bpe.rs)
  * Reads HEX-encoded vocab.json + merges.txt
  * Detects id collisions, rejects orphan merges
  * 2 new round-trip tests PASS

- `apr tokenize encode-corpus` CLI subcommand
  (crates/apr-cli/src/commands/tokenize.rs::run_encode_corpus,
   crates/apr-cli/src/tokenize_commands.rs,
   crates/apr-cli/src/dispatch_analysis.rs)
  * Gated `#[cfg(feature = "training")]`
  * Writes `shard-NNNNN.bin` (u32 LE) + `manifest.json` (schema
    `pretokenize-bin-v1`)
  * Flags: --corpus --tokenizer --output --shard-tokens
    --content-field --normalization --eos-policy
  * EOS lookup order: `</s>`, `<|endoftext|>`, `<eos>`, `<|eos|>`
  * "between" policy fix: emit EOS BEFORE each doc except the
    first (N-1 separators for N docs)

- `tests/pretokenize_shard_roundtrip.rs`
  * `cli_shard_layout_is_read_by_shard_batch_iter`
    — INV-PRETOK-002 + INV-PRETOK-007
  * `multi_shard_names_preserve_order` — INV-PRETOK-004

- `evidence/ship-two-001/pretokenize-bin-v1-partial-discharge.json`
  documents algorithm-level partial discharge.

Manual dogfood: 5-doc fixture → 78 tokens / 1 shard / 312 bytes /
4 EOS separators (N-1 for between-policy) / EOS id = 2 (`</s>`).

Next session: wait on task #118 (50257-vocab tokenizer training,
PID 2832743, 79min+) then run `apr tokenize encode-corpus` on
CSN-Python train split and dispatch to lambda-labs RTX 4090.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>