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.

backend/src/ely_eye/migrations.py

@@ -135,10 +135,7 @@ tokenize = 'unicode61'
 -- per CJK character and per identifier fragment, which is what makes those queries match.
 """
 
-# A memory is usable now when nothing has closed it, it had begun by now, and its
-# retention has not lapsed. Unknown bounds read as visible: absence of evidence about
-# when a legacy row was true is not evidence that it is false. The clock is formatted to
-# match how Python writes an aware datetime, so the comparison is exact to the millisecond.
+# A memory is usable now when nothing closed it, it had begun by now, and its retention has not lapsed; unknown bounds read as visible, because silence about when a legacy row was true is not evidence that it is false.
 VIEWS = """
     CREATE VIEW IF NOT EXISTS v_atoms_current AS
     SELECT * FROM atoms
@@ -153,8 +150,7 @@ VIEWS = """
     CREATE INDEX IF NOT EXISTS idx_atoms_valid_to ON atoms(valid_to);
 """
 
-# Columns the first version lacked, in the order they are added. Every one is nullable
-# or has a default, so an existing row survives the upgrade with its meaning intact.
+# Columns the first version lacked, in the order added; each is nullable or defaulted so an existing row keeps its meaning.
 _V1_TO_V2_COLUMNS = (
     ("holder_id", "TEXT NOT NULL DEFAULT ''"),
     ("origin", "TEXT NOT NULL DEFAULT 'artifact'"),