refactor: use WithRepo instead of WithDir for most git operations, clean up model migrations (#38555)

by the way, remove some unnecessary "models" imports from model
migration package, fix migration test model init bug
(modelmigration/migrationtest/tests.go)

services/repository/files/patch.go

@@ -168,7 +168,7 @@ func ApplyDiffPatch(ctx context.Context, repo *repo_model.Repository, doer *user
 		cmdApply.AddArguments("-3")
 	}
 
-	if err := cmdApply.WithDir(t.basePath).
+	if err := cmdApply.WithRepo(t.gitRepo).
 		WithStdinBytes([]byte(opts.Content)).
 		RunWithStderr(ctx); err != nil {
 		return nil, fmt.Errorf("git apply error: %w", err)