flat.Delete leaves AlreadyIndexed() live-vector count stale

#!/usr/bin/env python3
import os
import subprocess
import sys
from pathlib import Path

root = Path(os.environ.get("WEAVIATE_ROOT", ".")).resolve()
test_file = root / "adapters/repos/db/vector/flat/audit_delete_count_test.go"

go_test = r'''
package flat

import (
    "context"
    "fmt"
    "testing"

    "github.com/sirupsen/logrus/hooks/test"
    "github.com/stretchr/testify/require"
    "github.com/weaviate/weaviate/adapters/repos/db/lsmkv"
    "github.com/weaviate/weaviate/adapters/repos/db/vector/hnsw/distancer"
    flatent "github.com/weaviate/weaviate/entities/vectorindex/flat"
)

func TestFlatDeleteCount(t *testing.T) {
    logger, _ := test.NewNullLogger()
    root := t.TempDir()
    store := testStore(t, root, logger)
    defer store.Shutdown(context.Background())

    cfg := flatent.UserConfig{}
    cfg.SetDefaults()

    idx, err := New(Config{
        ID: "audit",
        RootPath: root,
        DistanceProvider: distancer.NewCosineDistanceProvider(),
        MakeBucketOptions: lsmkv.MakeRegularBucketOptions,
    }, cfg, store)
    require.NoError(t, err)
    defer idx.Shutdown(context.Background())

    require.NoError(t, idx.Add(context.Background(), 7, []float32{1, 0}))
    require.NoError(t, idx.Add(context.Background(), 8, []float32{0, 1}))

    before := idx.AlreadyIndexed()
    require.NoError(t, idx.Delete(7))
    after := idx.AlreadyIndexed()

    fmt.Printf(
        "before=%d after=%d contains_deleted=%v remaining=%v\n",
        before, after, idx.ContainsDoc(7), idx.ContainsDoc(8),
    )

    if before != 2 || after != 1 ||
        idx.ContainsDoc(7) || !idx.ContainsDoc(8) {
        t.Fatalf("unexpected live-vector state")
    }
}
'''

if not (root / "go.mod").exists():
    print("WEAVIATE_ROOT must point to a Weaviate checkout", file=sys.stderr)
    sys.exit(2)

test_file.write_text(go_test)

try:
    result = subprocess.run(
        [
            os.environ.get("GO", "go"),
            "test",
            "./adapters/repos/db/vector/flat",
            "-run",
            "^TestFlatDeleteCount$",
            "-count=1",
            "-v",
        ],
        cwd=root,
        text=True,
        capture_output=True,
    )
finally:
    test_file.unlink(missing_ok=True)

print(result.stdout, end="")
print(result.stderr, end="", file=sys.stderr)

if (
    result.returncode == 1
    and "before=2 after=2 contains_deleted=false remaining=true" in result.stdout
):
    print("BUG REPRODUCED")
    sys.exit(0)

if result.returncode == 0 and "before=2 after=1" in result.stdout:
    print("BUG NOT REPRODUCED")
    sys.exit(1)

print("ENVIRONMENT OR ORACLE FAILURE", file=sys.stderr)
sys.exit(2)

WEAVIATE_ROOT=/path/to/weaviate python3 repro.py

Add(7)
Add(8)
Delete(7)

before=2 after=1 contains_deleted=false remaining=true

AlreadyIndexed() == 1
ContainsDoc(7) == false
ContainsDoc(8) == true

before=2 after=2 contains_deleted=false remaining=true