rename estimator, skip unused cargo calc, fix six review bugs, close three seed guardrail holes

Rename: _stub_estimate -> _estimate_physics (it's a real deterministic
physics engine now, not a stub) and estimation_method "stub" ->
"physics_calc" to match the value pass 3 already used, for consistency
between the raw-estimate and scored-metric tables. Also skip the
cargo_capacity/cargo_capacity_kg arithmetic entirely in
_raw_physics_from_masses for domains that score neither and don't need
it as cost_efficiency's $/(kg·m) denominator either -- real but modest
savings on the ~11,000-eval-per-combo optimizer hot path (a separate
log1p-caching attempt was tried and reverted: it measured SLOWER, not
faster -- the extra dict lookup cost more than the two math.log1p calls
it avoided).

Six bugs found by a full-codebase review agent, verified individually:

- pipeline.py: LLM rate-limit retry called review_plausibility() with
  domain.metric_bounds instead of domain, crashing the whole pipeline
  run on any retry (every provider immediately accesses domain.name/
  .metric_bounds on that arg).
- _explore_result.html: mass-bar width divided by total_mass with no
  zero guard; biological/ambient actuators can legitimately have 0 mass
  floors, so an all-zero slider combination 500'd the explore endpoint.
- routes/pipeline.py: if init_db/Repository(conn) raised before
  repo/conn were assigned, the except/finally handlers referencing them
  raised UnboundLocalError, silently swallowed by bare except/pass --
  a bad PHYSCOM_DB path left a run stuck at status=pending forever with
  no diagnostic. conn/repo now init to None and are guarded before use;
  the truly-unreachable-DB case at least logs server-side now.
- repository.py: update_combination_status's downgrade guard protected
  scored/llm_reviewed/*_fail but not a write of "valid" -- pass 1
  re-running for a different domain against an already-reviewed combo
  silently reverted its status back to "valid", erasing the review
  signal. Verified directly: marked a combo reviewed, re-ran pass 1,
  status held.
- pipeline.py: cost_efficiency's operating-cost term fell back to
  ground rolling-resistance physics (effective_k_med or ...["ground"])
  for media with no resistance model (space), instead of skipping the
  term the way range_fuel explicitly does two lines above. Every scored
  interplanetary_travel combo got a cost_efficiency computed from
  ground physics applied to a spacecraft. Now reports amortized/upfront
  cost only for such media -- an honest partial answer.
- pipeline.py: `if min_accel and specific_thrust:` used truthiness
  instead of `is not None` -- dep_value() legitimately returns 0.0 for
  a declared floor of zero (Spaceship declares min_effective_accel=0),
  masking a real requirement as "undeclared."

Three seed-data guardrail holes, matching LOGIC DOCS/002's "missing
floor is a silent hole" pattern:

- constraint_resolver.py: CATEGORY_SEVERITY had no entry for the
  "material" category, so Nuclear Thermal Drive/Nuclear Fuel's
  radiation_shielding requirement defaulted to a non-blocking "warn"
  nothing in the catalog ever satisfies. Added material -> block.
  Consequence, verified: every nuclear combo across all domains now
  correctly fails pass 1, since nothing currently provides shielding --
  the accurate state given the catalog gap, not a regression.
- transport_example.py: Submarine had a mass range_min but no
  range_max, unlike its sibling water platform -- _decide_masses skips
  its entire structural-feasibility search when p_max is None. Added a
  20,000,000kg ceiling (small submersible to large ballistic-missile
  class).
- transport_example.py: Amphibious Vehicle declared no medium requires
  at all, so it vacuously satisfied every domain's medium constraint
  including space-only interplanetary_travel. Added medium=ground
  (the current requires model has no OR semantics for "ground or
  water," so this is a real tradeoff -- it can no longer participate in
  maritime_shipping either, losing the water half of "amphibious").
  Verified: interplanetary_travel's pass-2-estimated count dropped from
  33 to 3, and all 3 remaining are genuinely Spaceship-based; the ~30
  removed were confirmed to be Amphibious Vehicle's vacuous passes.

Logged the GPU-batching-for-the-optimizer discussion (why it doesn't
fit at current scale, what threshold would change that, what it would
actually require) as LOGIC DOCS/003 for future reference.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

CLAUDE.md

@@ -60,7 +60,7 @@ tests/                     # pytest, uses seeded_repo fixture from conftest.py
 ## Data flow (pipeline passes)
 
 1. **Pass 1 — Constraints**: `ConstraintResolver.resolve()` → blocked/conditional/valid. Blocked combos get a result row and `continue`.
-2. **Pass 2 — Estimation**: LLM or `_stub_estimate()` → raw metric values. Saved immediately via `save_raw_estimates()` (normalized_score=NULL).
+2. **Pass 2 — Estimation**: `_estimate_physics()` (deterministic physics engine; estimator-only, no LLM) → raw metric values. Saved immediately via `save_raw_estimates()` (normalized_score=NULL).
 3. **Pass 3 — Scoring**: `Scorer.score_combination()` → log-normalized scores + weighted geometric mean composite. Saves via `save_scores()` + `save_result()`.
 4. **Pass 4 — LLM Review**: Only for above-threshold combos with an LLM provider. No real provider yet (only `MockLLMProvider`).
 5. **Pass 5 — Human Review**: Manual via web UI results page.