Remove GetByBean method because sometimes it's danger when query condition parameter is zero and also introduce new generic methods (#28220)

The function `GetByBean` has an obvious defect that when the fields are
empty values, it will be ignored. Then users will get a wrong result
which is possibly used to make a security problem.

To avoid the possibility, this PR removed function `GetByBean` and all
references.
And some new generic functions have been introduced to be used.

The recommand usage like below.

```go
// if query an object according id
obj, err := db.GetByID[Object](ctx, id)
// query with other conditions
obj, err := db.Get[Object](ctx, builder.Eq{"a": a, "b":b})
```

services/pull/lfs.go

@@ -127,9 +127,7 @@ func createLFSMetaObjectsFromCatFileBatch(ctx context.Context, catFileBatchReade
 		// OK we have a pointer that is associated with the head repo
 		// and is actually a file in the LFS
 		// Therefore it should be associated with the base repo
-		meta := &git_model.LFSMetaObject{Pointer: pointer}
-		meta.RepositoryID = pr.BaseRepoID
-		if _, err := git_model.NewLFSMetaObject(ctx, meta); err != nil {
+		if _, err := git_model.NewLFSMetaObject(ctx, pr.BaseRepoID, pointer); err != nil {
 			_ = catFileBatchReader.CloseWithError(err)
 			break
 		}