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/update.go

@@ -438,7 +438,7 @@ func CreateOrUpdateFile(ctx context.Context, t *TemporaryUploadRepository, file
 
 	if lfsMetaObject != nil {
 		// We have an LFS object - create it
-		lfsMetaObject, err = git_model.NewLFSMetaObject(ctx, lfsMetaObject)
+		lfsMetaObject, err = git_model.NewLFSMetaObject(ctx, lfsMetaObject.RepositoryID, lfsMetaObject.Pointer)
 		if err != nil {
 			return err
 		}