Fix #732: Add LFS objects to base repository on merging (#7082)

On merge we walk the merge history and ensure that all lfs objects pointed to in
the history are added to the base repository. This switches from relying on having git-lfs installed on the server, (and in fact .gitattributes being correctly installed.)

7 files changed, 648 insertions, 292 deletions

diff --git a/integrations/api_helper_for_declarative_test.go b/integrations/api_helper_for_declarative_test.go
index 85f0ab621f..42c271e3af 100644
--- a/integrations/api_helper_for_declarative_test.go
+++ b/integrations/api_helper_for_declarative_test.go
@@ -66,6 +66,44 @@ func doAPICreateRepository(ctx APITestContext, empty bool, callback ...func(*tes
 	}
 }
 
+func doAPIAddCollaborator(ctx APITestContext, username string, mode models.AccessMode) func(*testing.T) {
+	return func(t *testing.T) {
+		permission := "read"
+
+		if mode == models.AccessModeAdmin {
+			permission = "admin"
+		} else if mode > models.AccessModeRead {
+			permission = "write"
+		}
+		addCollaboratorOption := &api.AddCollaboratorOption{
+			Permission: &permission,
+		}
+		req := NewRequestWithJSON(t, "PUT", fmt.Sprintf("/api/v1/repos/%s/%s/collaborators/%s?token=%s", ctx.Username, ctx.Reponame, username, ctx.Token), addCollaboratorOption)
+		if ctx.ExpectedCode != 0 {
+			ctx.Session.MakeRequest(t, req, ctx.ExpectedCode)
+			return
+		}
+		ctx.Session.MakeRequest(t, req, http.StatusNoContent)
+	}
+}
+
+func doAPIForkRepository(ctx APITestContext, username string, callback ...func(*testing.T, api.Repository)) func(*testing.T) {
+	return func(t *testing.T) {
+		createForkOption := &api.CreateForkOption{}
+		req := NewRequestWithJSON(t, "POST", fmt.Sprintf("/api/v1/repos/%s/%s/forks?token=%s", username, ctx.Reponame, ctx.Token), createForkOption)
+		if ctx.ExpectedCode != 0 {
+			ctx.Session.MakeRequest(t, req, ctx.ExpectedCode)
+			return
+		}
+		resp := ctx.Session.MakeRequest(t, req, http.StatusAccepted)
+		var repository api.Repository
+		DecodeJSON(t, resp, &repository)
+		if len(callback) > 0 {
+			callback[0](t, repository)
+		}
+	}
+}
+
 func doAPIGetRepository(ctx APITestContext, callback ...func(*testing.T, api.Repository)) func(*testing.T) {
 	return func(t *testing.T) {
 		urlStr := fmt.Sprintf("/api/v1/repos/%s/%s?token=%s", ctx.Username, ctx.Reponame, ctx.Token)
diff --git a/integrations/git_test.go b/integrations/git_test.go
index ce5aee493d..8578fb86d5 100644
--- a/integrations/git_test.go
+++ b/integrations/git_test.go
@@ -39,17 +39,23 @@ func testGit(t *testing.T, u *url.URL) {
 
 	u.Path = baseAPITestContext.GitPath()
 
+	forkedUserCtx := NewAPITestContext(t, "user4", "repo1")
+
 	t.Run("HTTP", func(t *testing.T) {
 		PrintCurrentTest(t)
+		ensureAnonymousClone(t, u)
 		httpContext := baseAPITestContext
 		httpContext.Reponame = "repo-tmp-17"
+		forkedUserCtx.Reponame = httpContext.Reponame
 
 		dstPath, err := ioutil.TempDir("", httpContext.Reponame)
 		assert.NoError(t, err)
 		defer os.RemoveAll(dstPath)
 
-		t.Run("CreateRepo", doAPICreateRepository(httpContext, false))
-		ensureAnonymousClone(t, u)
+		t.Run("CreateRepoInDifferentUser", doAPICreateRepository(forkedUserCtx, false))
+		t.Run("AddUserAsCollaborator", doAPIAddCollaborator(forkedUserCtx, httpContext.Username, models.AccessModeRead))
+
+		t.Run("ForkFromDifferentUser", doAPIForkRepository(httpContext, forkedUserCtx.Username))
 
 		u.Path = httpContext.GitPath()
 		u.User = url.UserPassword(username, userPassword)
@@ -62,12 +68,23 @@ func testGit(t *testing.T, u *url.URL) {
 		mediaTest(t, &httpContext, little, big, littleLFS, bigLFS)
 
 		t.Run("BranchProtectMerge", doBranchProtectPRMerge(&httpContext, dstPath))
+		t.Run("MergeFork", func(t *testing.T) {
+			t.Run("CreatePRAndMerge", doMergeFork(httpContext, forkedUserCtx, "master", httpContext.Username+":master"))
+			t.Run("DeleteRepository", doAPIDeleteRepository(httpContext))
+			rawTest(t, &forkedUserCtx, little, big, littleLFS, bigLFS)
+			mediaTest(t, &forkedUserCtx, little, big, littleLFS, bigLFS)
+		})
 	})
 	t.Run("SSH", func(t *testing.T) {
 		PrintCurrentTest(t)
 		sshContext := baseAPITestContext
 		sshContext.Reponame = "repo-tmp-18"
 		keyname := "my-testing-key"
+		forkedUserCtx.Reponame = sshContext.Reponame
+		t.Run("CreateRepoInDifferentUser", doAPICreateRepository(forkedUserCtx, false))
+		t.Run("AddUserAsCollaborator", doAPIAddCollaborator(forkedUserCtx, sshContext.Username, models.AccessModeRead))
+		t.Run("ForkFromDifferentUser", doAPIForkRepository(sshContext, forkedUserCtx.Username))
+
 		//Setup key the user ssh key
 		withKeyFile(t, keyname, func(keyFile string) {
 			t.Run("CreateUserKey", doAPICreateUserKey(sshContext, "test-key", keyFile))
@@ -81,8 +98,6 @@ func testGit(t *testing.T, u *url.URL) {
 			assert.NoError(t, err)
 			defer os.RemoveAll(dstPath)
 
-			t.Run("CreateRepo", doAPICreateRepository(sshContext, false))
-
 			t.Run("Clone", doGitClone(dstPath, sshURL))
 
 			little, big := standardCommitAndPushTest(t, dstPath)
@@ -91,8 +106,13 @@ func testGit(t *testing.T, u *url.URL) {
 			mediaTest(t, &sshContext, little, big, littleLFS, bigLFS)
 
 			t.Run("BranchProtectMerge", doBranchProtectPRMerge(&sshContext, dstPath))
+			t.Run("MergeFork", func(t *testing.T) {
+				t.Run("CreatePRAndMerge", doMergeFork(sshContext, forkedUserCtx, "master", sshContext.Username+":master"))
+				t.Run("DeleteRepository", doAPIDeleteRepository(sshContext))
+				rawTest(t, &forkedUserCtx, little, big, littleLFS, bigLFS)
+				mediaTest(t, &forkedUserCtx, little, big, littleLFS, bigLFS)
+			})
 		})
-
 	})
 }
 
@@ -341,3 +361,16 @@ func doProtectBranch(ctx APITestContext, branch string, userToWhitelist string)
 		assert.EqualValues(t, "success%3DBranch%2Bprotection%2Bfor%2Bbranch%2B%2527"+url.QueryEscape(branch)+"%2527%2Bhas%2Bbeen%2Bupdated.", flashCookie.Value)
 	}
 }
+
+func doMergeFork(ctx, baseCtx APITestContext, baseBranch, headBranch string) func(t *testing.T) {
+	return func(t *testing.T) {
+		var pr api.PullRequest
+		var err error
+		t.Run("CreatePullRequest", func(t *testing.T) {
+			pr, err = doAPICreatePullRequest(ctx, baseCtx.Username, baseCtx.Reponame, baseBranch, headBranch)(t)
+			assert.NoError(t, err)
+		})
+		t.Run("MergePR", doAPIMergePullRequest(baseCtx, baseCtx.Username, baseCtx.Reponame, pr.Index))
+
+	}
+}
diff --git a/models/pull.go b/models/pull.go
index e5d421e6ba..38976d37ec 100644
--- a/models/pull.go
+++ b/models/pull.go
@@ -7,7 +7,6 @@ package models
 
 import (
 	"bufio"
-	"bytes"
 	"fmt"
 	"io/ioutil"
 	"os"
@@ -18,7 +17,6 @@ import (
 	"time"
 
 	"code.gitea.io/gitea/modules/base"
-	"code.gitea.io/gitea/modules/cache"
 	"code.gitea.io/gitea/modules/git"
 	"code.gitea.io/gitea/modules/log"
 	"code.gitea.io/gitea/modules/process"
@@ -368,288 +366,8 @@ func (pr *PullRequest) CheckUserAllowedToMerge(doer *User) (err error) {
 	return nil
 }
 
-func getDiffTree(repoPath, baseBranch, headBranch string) (string, error) {
-	getDiffTreeFromBranch := func(repoPath, baseBranch, headBranch string) (string, error) {
-		var outbuf, errbuf strings.Builder
-		// Compute the diff-tree for sparse-checkout
-		// The branch argument must be enclosed with double-quotes ("") in case it contains slashes (e.g "feature/test")
-		if err := git.NewCommand("diff-tree", "--no-commit-id", "--name-only", "-r", "--root", baseBranch, headBranch).RunInDirPipeline(repoPath, &outbuf, &errbuf); err != nil {
-			return "", fmt.Errorf("git diff-tree [%s base:%s head:%s]: %s", repoPath, baseBranch, headBranch, errbuf.String())
-		}
-		return outbuf.String(), nil
-	}
-
-	list, err := getDiffTreeFromBranch(repoPath, baseBranch, headBranch)
-	if err != nil {
-		return "", err
-	}
-
-	// Prefixing '/' for each entry, otherwise all files with the same name in subdirectories would be matched.
-	out := bytes.Buffer{}
-	scanner := bufio.NewScanner(strings.NewReader(list))
-	for scanner.Scan() {
-		fmt.Fprintf(&out, "/%s\n", scanner.Text())
-	}
-	return out.String(), nil
-}
-
-// Merge merges pull request to base repository.
-// FIXME: add repoWorkingPull make sure two merges does not happen at same time.
-func (pr *PullRequest) Merge(doer *User, baseGitRepo *git.Repository, mergeStyle MergeStyle, message string) (err error) {
-	if err = pr.GetHeadRepo(); err != nil {
-		return fmt.Errorf("GetHeadRepo: %v", err)
-	} else if err = pr.GetBaseRepo(); err != nil {
-		return fmt.Errorf("GetBaseRepo: %v", err)
-	}
-
-	prUnit, err := pr.BaseRepo.GetUnit(UnitTypePullRequests)
-	if err != nil {
-		return err
-	}
-	prConfig := prUnit.PullRequestsConfig()
-
-	if err := pr.CheckUserAllowedToMerge(doer); err != nil {
-		return fmt.Errorf("CheckUserAllowedToMerge: %v", err)
-	}
-
-	// Check if merge style is correct and allowed
-	if !prConfig.IsMergeStyleAllowed(mergeStyle) {
-		return ErrInvalidMergeStyle{pr.BaseRepo.ID, mergeStyle}
-	}
-
-	defer func() {
-		go HookQueue.Add(pr.BaseRepo.ID)
-		go AddTestPullRequestTask(doer, pr.BaseRepo.ID, pr.BaseBranch, false)
-	}()
-
-	// Clone base repo.
-	tmpBasePath, err := CreateTemporaryPath("merge")
-	if err != nil {
-		return err
-	}
-	defer func() {
-		if err := RemoveTemporaryPath(tmpBasePath); err != nil {
-			log.Error("Merge: RemoveTemporaryPath: %s", err)
-		}
-	}()
-
-	headRepoPath := RepoPath(pr.HeadUserName, pr.HeadRepo.Name)
-
-	if err := git.Clone(baseGitRepo.Path, tmpBasePath, git.CloneRepoOptions{
-		Shared:     true,
-		NoCheckout: true,
-		Branch:     pr.BaseBranch,
-	}); err != nil {
-		return fmt.Errorf("git clone: %v", err)
-	}
-
-	remoteRepoName := "head_repo"
-
-	// Add head repo remote.
-	addCacheRepo := func(staging, cache string) error {
-		p := filepath.Join(staging, ".git", "objects", "info", "alternates")
-		f, err := os.OpenFile(p, os.O_APPEND|os.O_WRONLY, 0600)
-		if err != nil {
-			return err
-		}
-		defer f.Close()
-		data := filepath.Join(cache, "objects")
-		if _, err := fmt.Fprintln(f, data); err != nil {
-			return err
-		}
-		return nil
-	}
-
-	if err := addCacheRepo(tmpBasePath, headRepoPath); err != nil {
-		return fmt.Errorf("addCacheRepo [%s -> %s]: %v", headRepoPath, tmpBasePath, err)
-	}
-
-	var errbuf strings.Builder
-	if err := git.NewCommand("remote", "add", remoteRepoName, headRepoPath).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-		return fmt.Errorf("git remote add [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-	}
-
-	// Fetch head branch
-	if err := git.NewCommand("fetch", remoteRepoName).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-		return fmt.Errorf("git fetch [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-	}
-
-	trackingBranch := path.Join(remoteRepoName, pr.HeadBranch)
-	stagingBranch := fmt.Sprintf("%s_%s", remoteRepoName, pr.HeadBranch)
-
-	// Enable sparse-checkout
-	sparseCheckoutList, err := getDiffTree(tmpBasePath, pr.BaseBranch, trackingBranch)
-	if err != nil {
-		return fmt.Errorf("getDiffTree: %v", err)
-	}
-
-	infoPath := filepath.Join(tmpBasePath, ".git", "info")
-	if err := os.MkdirAll(infoPath, 0700); err != nil {
-		return fmt.Errorf("creating directory failed [%s]: %v", infoPath, err)
-	}
-	sparseCheckoutListPath := filepath.Join(infoPath, "sparse-checkout")
-	if err := ioutil.WriteFile(sparseCheckoutListPath, []byte(sparseCheckoutList), 0600); err != nil {
-		return fmt.Errorf("Writing sparse-checkout file to %s: %v", sparseCheckoutListPath, err)
-	}
-
-	if err := git.NewCommand("config", "--local", "core.sparseCheckout", "true").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-		return fmt.Errorf("git config [core.sparsecheckout -> true]: %v", errbuf.String())
-	}
-
-	// Read base branch index
-	if err := git.NewCommand("read-tree", "HEAD").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-		return fmt.Errorf("git read-tree HEAD: %s", errbuf.String())
-	}
-
-	// Merge commits.
-	switch mergeStyle {
-	case MergeStyleMerge:
-		if err := git.NewCommand("merge", "--no-ff", "--no-commit", trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git merge --no-ff --no-commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
-		}
-
-		sig := doer.NewGitSig()
-		if err := git.NewCommand("commit", fmt.Sprintf("--author='%s <%s>'", sig.Name, sig.Email), "-m", message).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
-		}
-	case MergeStyleRebase:
-		// Checkout head branch
-		if err := git.NewCommand("checkout", "-b", stagingBranch, trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git checkout: %s", errbuf.String())
-		}
-		// Rebase before merging
-		if err := git.NewCommand("rebase", "-q", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git rebase [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-		}
-		// Checkout base branch again
-		if err := git.NewCommand("checkout", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git checkout: %s", errbuf.String())
-		}
-		// Merge fast forward
-		if err := git.NewCommand("merge", "--ff-only", "-q", stagingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git merge --ff-only [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-		}
-	case MergeStyleRebaseMerge:
-		// Checkout head branch
-		if err := git.NewCommand("checkout", "-b", stagingBranch, trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git checkout: %s", errbuf.String())
-		}
-		// Rebase before merging
-		if err := git.NewCommand("rebase", "-q", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git rebase [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-		}
-		// Checkout base branch again
-		if err := git.NewCommand("checkout", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git checkout: %s", errbuf.String())
-		}
-		// Prepare merge with commit
-		if err := git.NewCommand("merge", "--no-ff", "--no-commit", "-q", stagingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git merge --no-ff [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-		}
-
-		// Set custom message and author and create merge commit
-		sig := doer.NewGitSig()
-		if err := git.NewCommand("commit", fmt.Sprintf("--author='%s <%s>'", sig.Name, sig.Email), "-m", message).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
-		}
-
-	case MergeStyleSquash:
-		// Merge with squash
-		if err := git.NewCommand("merge", "-q", "--squash", trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git merge --squash [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
-		}
-		sig := pr.Issue.Poster.NewGitSig()
-		if err := git.NewCommand("commit", fmt.Sprintf("--author='%s <%s>'", sig.Name, sig.Email), "-m", message).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
-			return fmt.Errorf("git commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
-		}
-	default:
-		return ErrInvalidMergeStyle{pr.BaseRepo.ID, mergeStyle}
-	}
-
-	env := PushingEnvironment(doer, pr.BaseRepo)
-
-	// Push back to upstream.
-	if err := git.NewCommand("push", baseGitRepo.Path, pr.BaseBranch).RunInDirTimeoutEnvPipeline(env, -1, tmpBasePath, nil, &errbuf); err != nil {
-		return fmt.Errorf("git push: %s", errbuf.String())
-	}
-
-	pr.MergedCommitID, err = baseGitRepo.GetBranchCommitID(pr.BaseBranch)
-	if err != nil {
-		return fmt.Errorf("GetBranchCommit: %v", err)
-	}
-
-	pr.MergedUnix = util.TimeStampNow()
-	pr.Merger = doer
-	pr.MergerID = doer.ID
-
-	if err = pr.setMerged(); err != nil {
-		log.Error("setMerged [%d]: %v", pr.ID, err)
-	}
-
-	if err = MergePullRequestAction(doer, pr.Issue.Repo, pr.Issue); err != nil {
-		log.Error("MergePullRequestAction [%d]: %v", pr.ID, err)
-	}
-
-	// Reset cached commit count
-	cache.Remove(pr.Issue.Repo.GetCommitsCountCacheKey(pr.BaseBranch, true))
-
-	// Reload pull request information.
-	if err = pr.LoadAttributes(); err != nil {
-		log.Error("LoadAttributes: %v", err)
-		return nil
-	}
-
-	mode, _ := AccessLevel(doer, pr.Issue.Repo)
-	if err = PrepareWebhooks(pr.Issue.Repo, HookEventPullRequest, &api.PullRequestPayload{
-		Action:      api.HookIssueClosed,
-		Index:       pr.Index,
-		PullRequest: pr.APIFormat(),
-		Repository:  pr.Issue.Repo.APIFormat(mode),
-		Sender:      doer.APIFormat(),
-	}); err != nil {
-		log.Error("PrepareWebhooks: %v", err)
-	} else {
-		go HookQueue.Add(pr.Issue.Repo.ID)
-	}
-
-	l, err := baseGitRepo.CommitsBetweenIDs(pr.MergedCommitID, pr.MergeBase)
-	if err != nil {
-		log.Error("CommitsBetweenIDs: %v", err)
-		return nil
-	}
-
-	// It is possible that head branch is not fully sync with base branch for merge commits,
-	// so we need to get latest head commit and append merge commit manually
-	// to avoid strange diff commits produced.
-	mergeCommit, err := baseGitRepo.GetBranchCommit(pr.BaseBranch)
-	if err != nil {
-		log.Error("GetBranchCommit: %v", err)
-		return nil
-	}
-	if mergeStyle == MergeStyleMerge {
-		l.PushFront(mergeCommit)
-	}
-
-	p := &api.PushPayload{
-		Ref:        git.BranchPrefix + pr.BaseBranch,
-		Before:     pr.MergeBase,
-		After:      mergeCommit.ID.String(),
-		CompareURL: setting.AppURL + pr.BaseRepo.ComposeCompareURL(pr.MergeBase, pr.MergedCommitID),
-		Commits:    ListToPushCommits(l).ToAPIPayloadCommits(pr.BaseRepo.HTMLURL()),
-		Repo:       pr.BaseRepo.APIFormat(mode),
-		Pusher:     pr.HeadRepo.MustOwner().APIFormat(),
-		Sender:     doer.APIFormat(),
-	}
-	if err = PrepareWebhooks(pr.BaseRepo, HookEventPush, p); err != nil {
-		log.Error("PrepareWebhooks: %v", err)
-	} else {
-		go HookQueue.Add(pr.BaseRepo.ID)
-	}
-	return nil
-}
-
-// setMerged sets a pull request to merged and closes the corresponding issue
-func (pr *PullRequest) setMerged() (err error) {
+// SetMerged sets a pull request to merged and closes the corresponding issue
+func (pr *PullRequest) SetMerged() (err error) {
 	if pr.HasMerged {
 		return fmt.Errorf("PullRequest[%d] already merged", pr.Index)
 	}
@@ -716,7 +434,7 @@ func (pr *PullRequest) manuallyMerged() bool {
 		pr.Merger = merger
 		pr.MergerID = merger.ID
 
-		if err = pr.setMerged(); err != nil {
+		if err = pr.SetMerged(); err != nil {
 			log.Error("PullRequest[%d].setMerged : %v", pr.ID, err)
 			return false
 		}
diff --git a/modules/pull/lfs.go b/modules/pull/lfs.go
new file mode 100644
index 0000000000..77890667d6
--- /dev/null
+++ b/modules/pull/lfs.go
@@ -0,0 +1,226 @@
+// Copyright 2019 The Gitea Authors.
+// All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package pull
+
+import (
+	"bufio"
+	"bytes"
+	"fmt"
+	"io"
+	"strconv"
+	"strings"
+	"sync"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/lfs"
+	"code.gitea.io/gitea/modules/log"
+)
+
+// LFSPush pushes lfs objects referred to in new commits in the head repository from the base repository
+func LFSPush(tmpBasePath, mergeHeadSHA, mergeBaseSHA string, pr *models.PullRequest) error {
+	// Now we have to implement git lfs push
+	// git rev-list --objects --filter=blob:limit=1k HEAD --not base
+	// pass blob shas in to git cat-file --batch-check (possibly unnecessary)
+	// ensure only blobs and <=1k size then pass in to git cat-file --batch
+	// to read each sha and check each as a pointer
+	// Then if they are lfs -> add them to the baseRepo
+	revListReader, revListWriter := io.Pipe()
+	shasToCheckReader, shasToCheckWriter := io.Pipe()
+	catFileCheckReader, catFileCheckWriter := io.Pipe()
+	shasToBatchReader, shasToBatchWriter := io.Pipe()
+	catFileBatchReader, catFileBatchWriter := io.Pipe()
+	errChan := make(chan error, 1)
+	wg := sync.WaitGroup{}
+	wg.Add(6)
+	// Create the go-routines in reverse order.
+
+	// 6. Take the output of cat-file --batch and check if each file in turn
+	// to see if they're pointers to files in the LFS store associated with
+	// the head repo and add them to the base repo if so
+	go readCatFileBatch(catFileBatchReader, &wg, pr)
+
+	// 5. Take the shas of the blobs and batch read them
+	go doCatFileBatch(shasToBatchReader, catFileBatchWriter, &wg, tmpBasePath)
+
+	// 4. From the provided objects restrict to blobs <=1k
+	go readCatFileBatchCheck(catFileCheckReader, shasToBatchWriter, &wg)
+
+	// 3. Run batch-check on the objects retrieved from rev-list
+	go doCatFileBatchCheck(shasToCheckReader, catFileCheckWriter, &wg, tmpBasePath)
+
+	// 2. Check each object retrieved rejecting those without names as they will be commits or trees
+	go readRevListObjects(revListReader, shasToCheckWriter, &wg)
+
+	// 1. Run rev-list objects from mergeHead to mergeBase
+	go doRevListObjects(revListWriter, &wg, tmpBasePath, mergeHeadSHA, mergeBaseSHA, errChan)
+
+	wg.Wait()
+	select {
+	case err, has := <-errChan:
+		if has {
+			return err
+		}
+	default:
+	}
+	return nil
+}
+
+func doRevListObjects(revListWriter *io.PipeWriter, wg *sync.WaitGroup, tmpBasePath, headSHA, baseSHA string, errChan chan<- error) {
+	defer wg.Done()
+	defer revListWriter.Close()
+	stderr := new(bytes.Buffer)
+	var errbuf strings.Builder
+	cmd := git.NewCommand("rev-list", "--objects", headSHA, "--not", baseSHA)
+	if err := cmd.RunInDirPipeline(tmpBasePath, revListWriter, stderr); err != nil {
+		log.Error("git rev-list [%s]: %v - %s", tmpBasePath, err, errbuf.String())
+		errChan <- fmt.Errorf("git rev-list [%s]: %v - %s", tmpBasePath, err, errbuf.String())
+	}
+}
+
+func readRevListObjects(revListReader *io.PipeReader, shasToCheckWriter *io.PipeWriter, wg *sync.WaitGroup) {
+	defer wg.Done()
+	defer revListReader.Close()
+	defer shasToCheckWriter.Close()
+	scanner := bufio.NewScanner(revListReader)
+	for scanner.Scan() {
+		line := scanner.Text()
+		if len(line) == 0 {
+			continue
+		}
+		fields := strings.Split(line, " ")
+		if len(fields) < 2 || len(fields[1]) == 0 {
+			continue
+		}
+		toWrite := []byte(fields[0] + "\n")
+		for len(toWrite) > 0 {
+			n, err := shasToCheckWriter.Write(toWrite)
+			if err != nil {
+				_ = revListReader.CloseWithError(err)
+				break
+			}
+			toWrite = toWrite[n:]
+		}
+	}
+	_ = shasToCheckWriter.CloseWithError(scanner.Err())
+}
+
+func doCatFileBatchCheck(shasToCheckReader *io.PipeReader, catFileCheckWriter *io.PipeWriter, wg *sync.WaitGroup, tmpBasePath string) {
+	defer wg.Done()
+	defer shasToCheckReader.Close()
+	defer catFileCheckWriter.Close()
+
+	stderr := new(bytes.Buffer)
+	var errbuf strings.Builder
+	cmd := git.NewCommand("cat-file", "--batch-check")
+	if err := cmd.RunInDirFullPipeline(tmpBasePath, catFileCheckWriter, stderr, shasToCheckReader); err != nil {
+		_ = catFileCheckWriter.CloseWithError(fmt.Errorf("git cat-file --batch-check [%s]: %v - %s", tmpBasePath, err, errbuf.String()))
+	}
+}
+
+func readCatFileBatchCheck(catFileCheckReader *io.PipeReader, shasToBatchWriter *io.PipeWriter, wg *sync.WaitGroup) {
+	defer wg.Done()
+	defer catFileCheckReader.Close()
+
+	scanner := bufio.NewScanner(catFileCheckReader)
+	defer func() {
+		_ = shasToBatchWriter.CloseWithError(scanner.Err())
+	}()
+	for scanner.Scan() {
+		line := scanner.Text()
+		if len(line) == 0 {
+			continue
+		}
+		fields := strings.Split(line, " ")
+		if len(fields) < 3 || fields[1] != "blob" {
+			continue
+		}
+		size, _ := strconv.Atoi(string(fields[2]))
+		if size > 1024 {
+			continue
+		}
+		toWrite := []byte(fields[0] + "\n")
+		for len(toWrite) > 0 {
+			n, err := shasToBatchWriter.Write(toWrite)
+			if err != nil {
+				_ = catFileCheckReader.CloseWithError(err)
+				break
+			}
+			toWrite = toWrite[n:]
+		}
+	}
+}
+
+func doCatFileBatch(shasToBatchReader *io.PipeReader, catFileBatchWriter *io.PipeWriter, wg *sync.WaitGroup, tmpBasePath string) {
+	defer wg.Done()
+	defer shasToBatchReader.Close()
+	defer catFileBatchWriter.Close()
+
+	stderr := new(bytes.Buffer)
+	var errbuf strings.Builder
+	if err := git.NewCommand("cat-file", "--batch").RunInDirFullPipeline(tmpBasePath, catFileBatchWriter, stderr, shasToBatchReader); err != nil {
+		_ = shasToBatchReader.CloseWithError(fmt.Errorf("git rev-list [%s]: %v - %s", tmpBasePath, err, errbuf.String()))
+	}
+}
+
+func readCatFileBatch(catFileBatchReader *io.PipeReader, wg *sync.WaitGroup, pr *models.PullRequest) {
+	defer wg.Done()
+	defer catFileBatchReader.Close()
+
+	bufferedReader := bufio.NewReader(catFileBatchReader)
+	buf := make([]byte, 1025)
+	for {
+		// File descriptor line: sha
+		_, err := bufferedReader.ReadString(' ')
+		if err != nil {
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+		// Throw away the blob
+		if _, err := bufferedReader.ReadString(' '); err != nil {
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+		sizeStr, err := bufferedReader.ReadString('\n')
+		if err != nil {
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+		size, err := strconv.Atoi(sizeStr[:len(sizeStr)-1])
+		if err != nil {
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+		pointerBuf := buf[:size+1]
+		if _, err := io.ReadFull(bufferedReader, pointerBuf); err != nil {
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+		pointerBuf = pointerBuf[:size]
+		// Now we need to check if the pointerBuf is an LFS pointer
+		pointer := lfs.IsPointerFile(&pointerBuf)
+		if pointer == nil {
+			continue
+		}
+		// Then we need to check that this pointer is in the db
+		if _, err := pr.HeadRepo.GetLFSMetaObjectByOid(pointer.Oid); err != nil {
+			if err == models.ErrLFSObjectNotExist {
+				log.Warn("During merge of: %d in %-v, there is a pointer to LFS Oid: %s which although present in the LFS store is not associated with the head repo %-v", pr.Index, pr.BaseRepo, pointer.Oid, pr.HeadRepo)
+				continue
+			}
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+		// OK we have a pointer that is associated with the head repo
+		// and is actually a file in the LFS
+		// Therefore it should be associated with the base repo
+		pointer.RepositoryID = pr.BaseRepoID
+		if _, err := models.NewLFSMetaObject(pointer); err != nil {
+			_ = catFileBatchReader.CloseWithError(err)
+			break
+		}
+	}
+}
diff --git a/modules/pull/merge.go b/modules/pull/merge.go
new file mode 100644
index 0000000000..e12ede81d6
--- /dev/null
+++ b/modules/pull/merge.go
@@ -0,0 +1,339 @@
+// Copyright 2019 The Gitea Authors.
+// All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package pull
+
+import (
+	"bufio"
+	"bytes"
+	"fmt"
+	"io/ioutil"
+	"os"
+	"path"
+	"path/filepath"
+	"strings"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/modules/cache"
+	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/log"
+	"code.gitea.io/gitea/modules/setting"
+	api "code.gitea.io/gitea/modules/structs"
+	"code.gitea.io/gitea/modules/util"
+)
+
+// Merge merges pull request to base repository.
+// FIXME: add repoWorkingPull make sure two merges does not happen at same time.
+func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repository, mergeStyle models.MergeStyle, message string) (err error) {
+	if err = pr.GetHeadRepo(); err != nil {
+		return fmt.Errorf("GetHeadRepo: %v", err)
+	} else if err = pr.GetBaseRepo(); err != nil {
+		return fmt.Errorf("GetBaseRepo: %v", err)
+	}
+
+	prUnit, err := pr.BaseRepo.GetUnit(models.UnitTypePullRequests)
+	if err != nil {
+		return err
+	}
+	prConfig := prUnit.PullRequestsConfig()
+
+	if err := pr.CheckUserAllowedToMerge(doer); err != nil {
+		return fmt.Errorf("CheckUserAllowedToMerge: %v", err)
+	}
+
+	// Check if merge style is correct and allowed
+	if !prConfig.IsMergeStyleAllowed(mergeStyle) {
+		return models.ErrInvalidMergeStyle{ID: pr.BaseRepo.ID, Style: mergeStyle}
+	}
+
+	defer func() {
+		go models.HookQueue.Add(pr.BaseRepo.ID)
+		go models.AddTestPullRequestTask(doer, pr.BaseRepo.ID, pr.BaseBranch, false)
+	}()
+
+	// Clone base repo.
+	tmpBasePath, err := models.CreateTemporaryPath("merge")
+	if err != nil {
+		return err
+	}
+
+	defer func() {
+		if err := models.RemoveTemporaryPath(tmpBasePath); err != nil {
+			log.Error("Merge: RemoveTemporaryPath: %s", err)
+		}
+	}()
+
+	headRepoPath := models.RepoPath(pr.HeadUserName, pr.HeadRepo.Name)
+
+	if err := git.Clone(baseGitRepo.Path, tmpBasePath, git.CloneRepoOptions{
+		Shared:     true,
+		NoCheckout: true,
+		Branch:     pr.BaseBranch,
+	}); err != nil {
+		return fmt.Errorf("git clone: %v", err)
+	}
+
+	remoteRepoName := "head_repo"
+
+	// Add head repo remote.
+	addCacheRepo := func(staging, cache string) error {
+		p := filepath.Join(staging, ".git", "objects", "info", "alternates")
+		f, err := os.OpenFile(p, os.O_APPEND|os.O_WRONLY, 0600)
+		if err != nil {
+			return err
+		}
+		defer f.Close()
+		data := filepath.Join(cache, "objects")
+		if _, err := fmt.Fprintln(f, data); err != nil {
+			return err
+		}
+		return nil
+	}
+
+	if err := addCacheRepo(tmpBasePath, headRepoPath); err != nil {
+		return fmt.Errorf("addCacheRepo [%s -> %s]: %v", headRepoPath, tmpBasePath, err)
+	}
+
+	var errbuf strings.Builder
+	if err := git.NewCommand("remote", "add", remoteRepoName, headRepoPath).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git remote add [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+	}
+
+	// Fetch head branch
+	if err := git.NewCommand("fetch", remoteRepoName).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git fetch [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+	}
+
+	trackingBranch := path.Join(remoteRepoName, pr.HeadBranch)
+	stagingBranch := fmt.Sprintf("%s_%s", remoteRepoName, pr.HeadBranch)
+
+	// Enable sparse-checkout
+	sparseCheckoutList, err := getDiffTree(tmpBasePath, pr.BaseBranch, trackingBranch)
+	if err != nil {
+		return fmt.Errorf("getDiffTree: %v", err)
+	}
+
+	infoPath := filepath.Join(tmpBasePath, ".git", "info")
+	if err := os.MkdirAll(infoPath, 0700); err != nil {
+		return fmt.Errorf("creating directory failed [%s]: %v", infoPath, err)
+	}
+	sparseCheckoutListPath := filepath.Join(infoPath, "sparse-checkout")
+	if err := ioutil.WriteFile(sparseCheckoutListPath, []byte(sparseCheckoutList), 0600); err != nil {
+		return fmt.Errorf("Writing sparse-checkout file to %s: %v", sparseCheckoutListPath, err)
+	}
+
+	// Switch off LFS process (set required, clean and smudge here also)
+	if err := git.NewCommand("config", "--local", "filter.lfs.process", "").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git config [filter.lfs.process -> <> ]: %v", errbuf.String())
+	}
+	if err := git.NewCommand("config", "--local", "filter.lfs.required", "false").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git config [filter.lfs.required -> <false> ]: %v", errbuf.String())
+	}
+	if err := git.NewCommand("config", "--local", "filter.lfs.clean", "").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git config [filter.lfs.clean -> <> ]: %v", errbuf.String())
+	}
+	if err := git.NewCommand("config", "--local", "filter.lfs.smudge", "").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git config [filter.lfs.smudge -> <> ]: %v", errbuf.String())
+	}
+
+	if err := git.NewCommand("config", "--local", "core.sparseCheckout", "true").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git config [core.sparsecheckout -> true]: %v", errbuf.String())
+	}
+
+	// Read base branch index
+	if err := git.NewCommand("read-tree", "HEAD").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git read-tree HEAD: %s", errbuf.String())
+	}
+
+	// Merge commits.
+	switch mergeStyle {
+	case models.MergeStyleMerge:
+		if err := git.NewCommand("merge", "--no-ff", "--no-commit", trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git merge --no-ff --no-commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
+		}
+
+		sig := doer.NewGitSig()
+		if err := git.NewCommand("commit", fmt.Sprintf("--author='%s <%s>'", sig.Name, sig.Email), "-m", message).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
+		}
+	case models.MergeStyleRebase:
+		// Checkout head branch
+		if err := git.NewCommand("checkout", "-b", stagingBranch, trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git checkout: %s", errbuf.String())
+		}
+		// Rebase before merging
+		if err := git.NewCommand("rebase", "-q", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git rebase [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+		}
+		// Checkout base branch again
+		if err := git.NewCommand("checkout", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git checkout: %s", errbuf.String())
+		}
+		// Merge fast forward
+		if err := git.NewCommand("merge", "--ff-only", "-q", stagingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git merge --ff-only [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+		}
+	case models.MergeStyleRebaseMerge:
+		// Checkout head branch
+		if err := git.NewCommand("checkout", "-b", stagingBranch, trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git checkout: %s", errbuf.String())
+		}
+		// Rebase before merging
+		if err := git.NewCommand("rebase", "-q", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git rebase [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+		}
+		// Checkout base branch again
+		if err := git.NewCommand("checkout", pr.BaseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git checkout: %s", errbuf.String())
+		}
+		// Prepare merge with commit
+		if err := git.NewCommand("merge", "--no-ff", "--no-commit", "-q", stagingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git merge --no-ff [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+		}
+
+		// Set custom message and author and create merge commit
+		sig := doer.NewGitSig()
+		if err := git.NewCommand("commit", fmt.Sprintf("--author='%s <%s>'", sig.Name, sig.Email), "-m", message).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
+		}
+
+	case models.MergeStyleSquash:
+		// Merge with squash
+		if err := git.NewCommand("merge", "-q", "--squash", trackingBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git merge --squash [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+		}
+		sig := pr.Issue.Poster.NewGitSig()
+		if err := git.NewCommand("commit", fmt.Sprintf("--author='%s <%s>'", sig.Name, sig.Email), "-m", message).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+			return fmt.Errorf("git commit [%s]: %v - %s", tmpBasePath, err, errbuf.String())
+		}
+	default:
+		return models.ErrInvalidMergeStyle{ID: pr.BaseRepo.ID, Style: mergeStyle}
+	}
+
+	// OK we should cache our current head and origin/headbranch
+	mergeHeadSHA, err := git.GetFullCommitID(tmpBasePath, "HEAD")
+	if err != nil {
+		return fmt.Errorf("Failed to get full commit id for HEAD: %v", err)
+	}
+	mergeBaseSHA, err := git.GetFullCommitID(tmpBasePath, "origin/"+pr.BaseBranch)
+	if err != nil {
+		return fmt.Errorf("Failed to get full commit id for origin/%s: %v", pr.BaseBranch, err)
+	}
+
+	// Now it's questionable about where this should go - either after or before the push
+	// I think in the interests of data safety - failures to push to the lfs should prevent
+	// the merge as you can always remerge.
+	if setting.LFS.StartServer {
+		if err := LFSPush(tmpBasePath, mergeHeadSHA, mergeBaseSHA, pr); err != nil {
+			return err
+		}
+	}
+
+	env := models.PushingEnvironment(doer, pr.BaseRepo)
+
+	// Push back to upstream.
+	if err := git.NewCommand("push", "origin", pr.BaseBranch).RunInDirTimeoutEnvPipeline(env, -1, tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git push: %s", errbuf.String())
+	}
+
+	pr.MergedCommitID, err = baseGitRepo.GetBranchCommitID(pr.BaseBranch)
+	if err != nil {
+		return fmt.Errorf("GetBranchCommit: %v", err)
+	}
+
+	pr.MergedUnix = util.TimeStampNow()
+	pr.Merger = doer
+	pr.MergerID = doer.ID
+
+	if err = pr.SetMerged(); err != nil {
+		log.Error("setMerged [%d]: %v", pr.ID, err)
+	}
+
+	if err = models.MergePullRequestAction(doer, pr.Issue.Repo, pr.Issue); err != nil {
+		log.Error("MergePullRequestAction [%d]: %v", pr.ID, err)
+	}
+
+	// Reset cached commit count
+	cache.Remove(pr.Issue.Repo.GetCommitsCountCacheKey(pr.BaseBranch, true))
+
+	// Reload pull request information.
+	if err = pr.LoadAttributes(); err != nil {
+		log.Error("LoadAttributes: %v", err)
+		return nil
+	}
+
+	mode, _ := models.AccessLevel(doer, pr.Issue.Repo)
+	if err = models.PrepareWebhooks(pr.Issue.Repo, models.HookEventPullRequest, &api.PullRequestPayload{
+		Action:      api.HookIssueClosed,
+		Index:       pr.Index,
+		PullRequest: pr.APIFormat(),
+		Repository:  pr.Issue.Repo.APIFormat(mode),
+		Sender:      doer.APIFormat(),
+	}); err != nil {
+		log.Error("PrepareWebhooks: %v", err)
+	} else {
+		go models.HookQueue.Add(pr.Issue.Repo.ID)
+	}
+
+	l, err := baseGitRepo.CommitsBetweenIDs(pr.MergedCommitID, pr.MergeBase)
+	if err != nil {
+		log.Error("CommitsBetweenIDs: %v", err)
+		return nil
+	}
+
+	// It is possible that head branch is not fully sync with base branch for merge commits,
+	// so we need to get latest head commit and append merge commit manually
+	// to avoid strange diff commits produced.
+	mergeCommit, err := baseGitRepo.GetBranchCommit(pr.BaseBranch)
+	if err != nil {
+		log.Error("GetBranchCommit: %v", err)
+		return nil
+	}
+	if mergeStyle == models.MergeStyleMerge {
+		l.PushFront(mergeCommit)
+	}
+
+	p := &api.PushPayload{
+		Ref:        git.BranchPrefix + pr.BaseBranch,
+		Before:     pr.MergeBase,
+		After:      mergeCommit.ID.String(),
+		CompareURL: setting.AppURL + pr.BaseRepo.ComposeCompareURL(pr.MergeBase, pr.MergedCommitID),
+		Commits:    models.ListToPushCommits(l).ToAPIPayloadCommits(pr.BaseRepo.HTMLURL()),
+		Repo:       pr.BaseRepo.APIFormat(mode),
+		Pusher:     pr.HeadRepo.MustOwner().APIFormat(),
+		Sender:     doer.APIFormat(),
+	}
+	if err = models.PrepareWebhooks(pr.BaseRepo, models.HookEventPush, p); err != nil {
+		log.Error("PrepareWebhooks: %v", err)
+	} else {
+		go models.HookQueue.Add(pr.BaseRepo.ID)
+	}
+	return nil
+}
+
+func getDiffTree(repoPath, baseBranch, headBranch string) (string, error) {
+	getDiffTreeFromBranch := func(repoPath, baseBranch, headBranch string) (string, error) {
+		var outbuf, errbuf strings.Builder
+		// Compute the diff-tree for sparse-checkout
+		// The branch argument must be enclosed with double-quotes ("") in case it contains slashes (e.g "feature/test")
+		if err := git.NewCommand("diff-tree", "--no-commit-id", "--name-only", "-r", "--root", baseBranch, headBranch).RunInDirPipeline(repoPath, &outbuf, &errbuf); err != nil {
+			return "", fmt.Errorf("git diff-tree [%s base:%s head:%s]: %s", repoPath, baseBranch, headBranch, errbuf.String())
+		}
+		return outbuf.String(), nil
+	}
+
+	list, err := getDiffTreeFromBranch(repoPath, baseBranch, headBranch)
+	if err != nil {
+		return "", err
+	}
+
+	// Prefixing '/' for each entry, otherwise all files with the same name in subdirectories would be matched.
+	out := bytes.Buffer{}
+	scanner := bufio.NewScanner(strings.NewReader(list))
+	for scanner.Scan() {
+		fmt.Fprintf(&out, "/%s\n", scanner.Text())
+	}
+	return out.String(), nil
+}
diff --git a/routers/api/v1/repo/pull.go b/routers/api/v1/repo/pull.go
index b14b0b02b8..d99c9a00c9 100644
--- a/routers/api/v1/repo/pull.go
+++ b/routers/api/v1/repo/pull.go
@@ -15,6 +15,7 @@ import (
 	"code.gitea.io/gitea/modules/git"
 	"code.gitea.io/gitea/modules/log"
 	"code.gitea.io/gitea/modules/notification"
+	"code.gitea.io/gitea/modules/pull"
 	api "code.gitea.io/gitea/modules/structs"
 	"code.gitea.io/gitea/modules/util"
 )
@@ -595,7 +596,7 @@ func MergePullRequest(ctx *context.APIContext, form auth.MergePullRequestForm) {
 		message += "\n\n" + form.MergeMessageField
 	}
 
-	if err := pr.Merge(ctx.User, ctx.Repo.GitRepo, models.MergeStyle(form.Do), message); err != nil {
+	if err := pull.Merge(pr, ctx.User, ctx.Repo.GitRepo, models.MergeStyle(form.Do), message); err != nil {
 		if models.IsErrInvalidMergeStyle(err) {
 			ctx.Status(405)
 			return
diff --git a/routers/repo/pull.go b/routers/repo/pull.go
index 5be8aa57c1..36b0d047b1 100644
--- a/routers/repo/pull.go
+++ b/routers/repo/pull.go
@@ -20,6 +20,7 @@ import (
 	"code.gitea.io/gitea/modules/git"
 	"code.gitea.io/gitea/modules/log"
 	"code.gitea.io/gitea/modules/notification"
+	"code.gitea.io/gitea/modules/pull"
 	"code.gitea.io/gitea/modules/setting"
 	"code.gitea.io/gitea/modules/util"
 
@@ -596,7 +597,7 @@ func MergePullRequest(ctx *context.Context, form auth.MergePullRequestForm) {
 		return
 	}
 
-	if err = pr.Merge(ctx.User, ctx.Repo.GitRepo, models.MergeStyle(form.Do), message); err != nil {
+	if err = pull.Merge(pr, ctx.User, ctx.Repo.GitRepo, models.MergeStyle(form.Do), message); err != nil {
 		if models.IsErrInvalidMergeStyle(err) {
 			ctx.Flash.Error(ctx.Tr("repo.pulls.invalid_merge_option"))
 			ctx.Redirect(ctx.Repo.RepoLink + "/pulls/" + com.ToStr(pr.Index))