diff --git a/modules/git/command.go b/modules/git/command.go
index c38fd0469..f095bb18b 100644
--- a/modules/git/command.go
+++ b/modules/git/command.go
@@ -221,8 +221,18 @@ type RunOpts struct {
 	Dir string
 
 	Stdout, Stderr io.Writer
-	Stdin          io.Reader
-	PipelineFunc   func(context.Context, context.CancelFunc) error
+
+	// Stdin is used for passing input to the command
+	// The caller must make sure the Stdin writer is closed properly to finish the Run function.
+	// Otherwise, the Run function may hang for long time or forever, especially when the Git's context deadline is not the same as the caller's.
+	// Some common mistakes:
+	// * `defer stdinWriter.Close()` then call `cmd.Run()`: the Run() would never return if the command is killed by timeout
+	// * `go { case <- parentContext.Done(): stdinWriter.Close() }` with `cmd.Run(DefaultTimeout)`: the command would have been killed by timeout but the Run doesn't return until stdinWriter.Close()
+	// * `go { if stdoutReader.Read() err != nil: stdinWriter.Close() }` with `cmd.Run()`: the stdoutReader may never return error if the command is killed by timeout
+	// In the future, ideally the git module itself should have full control of the stdin, to avoid such problems and make it easier to refactor to a better architecture.
+	Stdin io.Reader
+
+	PipelineFunc func(context.Context, context.CancelFunc) error
 }
 
 func commonBaseEnvs() []string {
diff --git a/modules/indexer/code/indexer.go b/modules/indexer/code/indexer.go
index 80bde7614..019773fe5 100644
--- a/modules/indexer/code/indexer.go
+++ b/modules/indexer/code/indexer.go
@@ -122,21 +122,6 @@ func Init() {
 			indexer := *globalIndexer.Load()
 			for _, indexerData := range items {
 				log.Trace("IndexerData Process Repo: %d", indexerData.RepoID)
-
-				// FIXME: it seems there is a bug in `CatFileBatch` or `nio.Pipe`, which will cause the process to hang forever in rare cases
-				/*
-					sync.(*Cond).Wait(cond.go:70)
-					github.com/djherbis/nio/v3.(*PipeReader).Read(sync.go:106)
-					bufio.(*Reader).fill(bufio.go:106)
-					bufio.(*Reader).ReadSlice(bufio.go:372)
-					bufio.(*Reader).collectFragments(bufio.go:447)
-					bufio.(*Reader).ReadString(bufio.go:494)
-					code.gitea.io/gitea/modules/git.ReadBatchLine(batch_reader.go:149)
-					code.gitea.io/gitea/modules/indexer/code.(*BleveIndexer).addUpdate(bleve.go:214)
-					code.gitea.io/gitea/modules/indexer/code.(*BleveIndexer).Index(bleve.go:296)
-					code.gitea.io/gitea/modules/indexer/code.(*wrappedIndexer).Index(wrapped.go:74)
-					code.gitea.io/gitea/modules/indexer/code.index(indexer.go:105)
-				*/
 				if err := index(ctx, indexer, indexerData.RepoID); err != nil {
 					unhandled = append(unhandled, indexerData)
 					if !setting.IsInTesting {