Fix LFS file not stored in LFS when uploaded/edited via API or web UI

modules/git/attribute/batch.go

@@ -36,7 +36,7 @@ func NewBatchChecker(repo *git.Repository, treeish string, attributes []string)
 		}
 	}()
 
-	cmd, envs, cleanup, err := checkAttrCommand(repo, treeish, nil, attributes)
+	cmd, envs, cleanup, err := checkAttrCommand(repo, treeish, nil, attributes, false)
 	if err != nil {
 		return nil, err
 	}

modules/git/attribute/checker.go

@@ -13,7 +13,7 @@ import (
 	"code.gitea.io/gitea/modules/git"
 )
 
-func checkAttrCommand(gitRepo *git.Repository, treeish string, filenames, attributes []string) (*git.Command, []string, func(), error) {
+func checkAttrCommand(gitRepo *git.Repository, treeish string, filenames, attributes []string, cached bool) (*git.Command, []string, func(), error) {
 	cancel := func() {}
 	envs := []string{"GIT_FLUSH=1"}
 	cmd := git.NewCommand("check-attr", "-z")
@@ -39,6 +39,10 @@ func checkAttrCommand(gitRepo *git.Repository, treeish string, filenames, attrib
 			)
 			cancel = deleteTemporaryFile
 		}
+	} else if cached {
+		// read from existing index instead of work tree, in cases where the repo is bare and has an index or the work tree
+		// contains unstaged changes that shouldn't affect the attribute check
+		cmd.AddArguments("--cached")
 	} // else: no treeish, assume it is a not a bare repo, read from working directory
 
 	cmd.AddDynamicArguments(attributes...)
@@ -51,12 +55,13 @@ func checkAttrCommand(gitRepo *git.Repository, treeish string, filenames, attrib
 type CheckAttributeOpts struct {
 	Filenames  []string
 	Attributes []string
+	Cached     bool
 }
 
 // CheckAttributes return the attributes of the given filenames and attributes in the given treeish.
 // If treeish is empty, then it will use current working directory, otherwise it will use the provided treeish on the bare repo
 func CheckAttributes(ctx context.Context, gitRepo *git.Repository, treeish string, opts CheckAttributeOpts) (map[string]*Attributes, error) {
-	cmd, envs, cancel, err := checkAttrCommand(gitRepo, treeish, opts.Filenames, opts.Attributes)
+	cmd, envs, cancel, err := checkAttrCommand(gitRepo, treeish, opts.Filenames, opts.Attributes, opts.Cached)
 	if err != nil {
 		return nil, err
 	}

modules/git/attribute/checker_test.go

@@ -57,8 +57,19 @@ func Test_Checker(t *testing.T) {
 		assert.Equal(t, expectedAttrs(), attrs["i-am-a-python.p"])
 	})
 
+	t.Run("Run git check-attr in bare repository using index", func(t *testing.T) {
+		attrs, err := CheckAttributes(t.Context(), gitRepo, "", CheckAttributeOpts{
+			Filenames:  []string{"i-am-a-python.p"},
+			Attributes: LinguistAttributes,
+			Cached:     true,
+		})
+		assert.NoError(t, err)
+		assert.Len(t, attrs, 1)
+		assert.Equal(t, expectedAttrs(), attrs["i-am-a-python.p"])
+	})
+
 	if !git.DefaultFeatures().SupportCheckAttrOnBare {
-		t.Skip("git version 2.40 is required to support run check-attr on bare repo")
+		t.Skip("git version 2.40 is required to support run check-attr on bare repo without using index")
 		return
 	}
 

services/repository/files/update.go

@@ -495,6 +495,8 @@ func CreateOrUpdateFile(ctx context.Context, t *TemporaryUploadRepository, file
 		attributesMap, err := attribute.CheckAttributes(ctx, t.gitRepo, "" /* use temp repo's working dir */, attribute.CheckAttributeOpts{
 			Attributes: []string{attribute.Filter},
 			Filenames:  []string{file.Options.treePath},
+			// An index is set, so it's okay to list the attributes from it
+			Cached: true,
 		})
 		if err != nil {
 			return err

services/repository/files/upload.go

@@ -107,10 +107,12 @@ func UploadRepoFiles(ctx context.Context, repo *repo_model.Repository, doer *use
 	}
 
 	var attributesMap map[string]*attribute.Attributes
-	if setting.LFS.StartServer {
+	if setting.LFS.StartServer && hasOldBranch {
 		attributesMap, err = attribute.CheckAttributes(ctx, t.gitRepo, "" /* use temp repo's working dir */, attribute.CheckAttributeOpts{
 			Attributes: []string{attribute.Filter},
 			Filenames:  names,
+			// An index is set, so it's okay to list the attributes from it
+			Cached: true,
 		})
 		if err != nil {
 			return err