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/repository/files/upload.go

@@ -143,7 +143,7 @@ func UploadRepoFiles(ctx context.Context, repo *repo_model.Repository, doer *use
 		if infos[i].lfsMetaObject == nil {
 			continue
 		}
-		infos[i].lfsMetaObject, err = git_model.NewLFSMetaObject(ctx, infos[i].lfsMetaObject)
+		infos[i].lfsMetaObject, err = git_model.NewLFSMetaObject(ctx, infos[i].lfsMetaObject.RepositoryID, infos[i].lfsMetaObject.Pointer)
 		if err != nil {
 			// OK Now we need to cleanup
 			return cleanUpAfterFailure(ctx, &infos, t, err)