Keep every file inside the rules the repo already wrote down

The 500-line rule and the one-line-comment rule were enforced only from
memory, so they drifted. bench/filesize_check.py now checks the budget on
every tracked source file, and it passes.

Split, with behaviour proven unchanged by comparing each moved function body
against HEAD byte for byte (53 training bodies, 21 benchmark bodies, 0
differences):

  db.py        503 -> 396   store_search.py     105
  bench/run.py 609 -> 351   query_set.py         80, report.py 211
  benchmarks.py 619 -> 424  benchmark_scoring.py 262
  training.py 1630 ->  94   training_{common,encode,metrics,datasets,lora,retrieval}

TrainingService stays as a thin facade for the CLI; the facade's parameter
lists are pinned against the module functions by inspect, which is what
catches a leaked self.

Deleted the eight top-level functions no file called, after fixing the scan
that had reported 201 false positives by skipping the defining file. The
v1/v2/v3 sweep found nothing to delete and says so: every remaining version
tag is an on-disk format marker, a migration step, a fixture name, or a
third-party model name.

Collapsed 39 multi-line comment blocks (86 lines) to one line each, keeping
the measured facts and error strings that justify the code.

269 tests pass; ruff clean; mypy 24 errors in 9 files against a 24-in-6
baseline, net zero; pyright 4, the same four HEAD measures.

bench/tests/test_joint.py

@@ -16,16 +16,9 @@ import numpy as np
 import pytest
 
 from bench import systems
-from bench.run import (
-    Query,
-    fingerprint,
-    latency,
-    load_rankings,
-    remeasure_latency,
-    scale_arm_names,
-    scale_probes,
-    write_markdown,
-)
+from bench.query_set import Query, scale_probes
+from bench.report import scale_arm_names, write_markdown
+from bench.run import fingerprint, latency, load_rankings, remeasure_latency
 from bench.systems import ARMS, ArmRunner, Atom, JointRunner
 from bench.tests.test_systems import ATOMS
 

bench/tests/test_systems.py

@@ -27,8 +27,7 @@ ATOMS = [
     Atom(atom_id="a3", source_id="src_red", text="the key hangs on the red door"),
 ]
 
-# The product names a source by content hash; the benchmark names the same file by
-# its corpus id (the source_id above). load_atoms joins the two through sources.path.
+# The product names a source by content hash, the benchmark by corpus id; load_atoms joins the two through sources.path.
 PRODUCT_SOURCES = {"prod_red_9f3a": "/fixture/red.png", "prod_blue_1c77": "/fixture/blue.png"}
 ATOM_PRODUCT_IDS = ["prod_red_9f3a", "prod_blue_1c77", "prod_red_9f3a"]
 
@@ -123,8 +122,7 @@ def test_load_atoms_returns_every_row_in_a_stable_order(tmp_path: Path, monkeypa
     make_database(db)
     loaded = load_atoms(db)
     assert [atom.atom_id for atom in loaded] == ["a1", "a2", "a3"]
-    # The database stores the product's content-hash id; the caller gets the corpus id
-    # the gold annotations use.
+    # The database stores the product's content-hash id; the caller gets the corpus id the gold annotations use.
     assert [atom.source_id for atom in loaded] == ["src_red", "src_blue", "src_red"]
     assert loaded[2].text == "the key hangs on the red door"