diff --git a/integrations/git_helper_for_declarative_test.go b/integrations/git_helper_for_declarative_test.go
index 9190d4bb4e5..d3f934d54c1 100644
--- a/integrations/git_helper_for_declarative_test.go
+++ b/integrations/git_helper_for_declarative_test.go
@@ -12,7 +12,9 @@ import (
 	"net/http"
 	"net/url"
 	"os"
+	"path"
 	"path/filepath"
+	"strings"
 	"testing"
 	"time"
 
@@ -36,7 +38,12 @@ func withKeyFile(t *testing.T, keyname string, callback func(string)) {
 	err = ssh.GenKeyPair(keyFile)
 	assert.NoError(t, err)
 
+	err = ioutil.WriteFile(path.Join(tmpDir, "ssh"), []byte("#!/bin/bash\n"+
+		"ssh -o \"UserKnownHostsFile=/dev/null\" -o \"StrictHostKeyChecking=no\" -o \"IdentitiesOnly=yes\" -i \""+keyFile+"\" \"$@\""), 0700)
+	assert.NoError(t, err)
+
 	//Setup ssh wrapper
+	os.Setenv("GIT_SSH", path.Join(tmpDir, "ssh"))
 	os.Setenv("GIT_SSH_COMMAND",
 		"ssh -o \"UserKnownHostsFile=/dev/null\" -o \"StrictHostKeyChecking=no\" -o \"IdentitiesOnly=yes\" -i \""+keyFile+"\"")
 	os.Setenv("GIT_SSH_VARIANT", "ssh")
@@ -53,6 +60,24 @@ func createSSHUrl(gitPath string, u *url.URL) *url.URL {
 	return &u2
 }
 
+func allowLFSFilters() []string {
+	// Now here we should explicitly allow lfs filters to run
+	globalArgs := git.GlobalCommandArgs
+	filteredLFSGlobalArgs := make([]string, len(git.GlobalCommandArgs))
+	j := 0
+	for _, arg := range git.GlobalCommandArgs {
+		if strings.Contains(arg, "lfs") {
+			j--
+		} else {
+			filteredLFSGlobalArgs[j] = arg
+			j++
+		}
+	}
+	filteredLFSGlobalArgs = filteredLFSGlobalArgs[:j]
+	git.GlobalCommandArgs = filteredLFSGlobalArgs
+	return globalArgs
+}
+
 func onGiteaRun(t *testing.T, callback func(*testing.T, *url.URL)) {
 	prepareTestEnv(t, 1)
 	s := http.Server{
@@ -78,7 +103,9 @@ func onGiteaRun(t *testing.T, callback func(*testing.T, *url.URL)) {
 
 func doGitClone(dstLocalPath string, u *url.URL) func(*testing.T) {
 	return func(t *testing.T) {
+		oldGlobals := allowLFSFilters()
 		assert.NoError(t, git.Clone(u.String(), dstLocalPath, git.CloneRepoOptions{}))
+		git.GlobalCommandArgs = oldGlobals
 		assert.True(t, com.IsExist(filepath.Join(dstLocalPath, "README.md")))
 	}
 }
@@ -139,7 +166,9 @@ func doGitCreateBranch(dstPath, branch string) func(*testing.T) {
 
 func doGitCheckoutBranch(dstPath string, args ...string) func(*testing.T) {
 	return func(t *testing.T) {
+		oldGlobals := allowLFSFilters()
 		_, err := git.NewCommand(append([]string{"checkout"}, args...)...).RunInDir(dstPath)
+		git.GlobalCommandArgs = oldGlobals
 		assert.NoError(t, err)
 	}
 }
@@ -153,7 +182,9 @@ func doGitMerge(dstPath string, args ...string) func(*testing.T) {
 
 func doGitPull(dstPath string, args ...string) func(*testing.T) {
 	return func(t *testing.T) {
+		oldGlobals := allowLFSFilters()
 		_, err := git.NewCommand(append([]string{"pull"}, args...)...).RunInDir(dstPath)
+		git.GlobalCommandArgs = oldGlobals
 		assert.NoError(t, err)
 	}
 }
diff --git a/integrations/git_test.go b/integrations/git_test.go
index 8578fb86d5d..dbcc2652276 100644
--- a/integrations/git_test.go
+++ b/integrations/git_test.go
@@ -19,6 +19,7 @@ import (
 
 	"code.gitea.io/gitea/models"
 	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/setting"
 	api "code.gitea.io/gitea/modules/structs"
 
 	"github.com/stretchr/testify/assert"
@@ -135,6 +136,11 @@ func standardCommitAndPushTest(t *testing.T, dstPath string) (little, big string
 func lfsCommitAndPushTest(t *testing.T, dstPath string) (littleLFS, bigLFS string) {
 	t.Run("LFS", func(t *testing.T) {
 		PrintCurrentTest(t)
+		setting.CheckLFSVersion()
+		if !setting.LFS.StartServer {
+			t.Skip()
+			return
+		}
 		prefix := "lfs-data-file-"
 		_, err := git.NewCommand("lfs").AddArguments("install").RunInDir(dstPath)
 		assert.NoError(t, err)
@@ -142,6 +148,21 @@ func lfsCommitAndPushTest(t *testing.T, dstPath string) (littleLFS, bigLFS strin
 		assert.NoError(t, err)
 		err = git.AddChanges(dstPath, false, ".gitattributes")
 		assert.NoError(t, err)
+		oldGlobals := allowLFSFilters()
+		err = git.CommitChanges(dstPath, git.CommitChangesOptions{
+			Committer: &git.Signature{
+				Email: "user2@example.com",
+				Name:  "User Two",
+				When:  time.Now(),
+			},
+			Author: &git.Signature{
+				Email: "user2@example.com",
+				Name:  "User Two",
+				When:  time.Now(),
+			},
+			Message: fmt.Sprintf("Testing commit @ %v", time.Now()),
+		})
+		git.GlobalCommandArgs = oldGlobals
 
 		littleLFS, bigLFS = commitAndPushTest(t, dstPath, prefix)
 
@@ -185,20 +206,25 @@ func rawTest(t *testing.T, ctx *APITestContext, little, big, littleLFS, bigLFS s
 		resp := session.MakeRequest(t, req, http.StatusOK)
 		assert.Equal(t, littleSize, resp.Body.Len())
 
-		req = NewRequest(t, "GET", path.Join("/", username, reponame, "/raw/branch/master/", littleLFS))
-		resp = session.MakeRequest(t, req, http.StatusOK)
-		assert.NotEqual(t, littleSize, resp.Body.Len())
-		assert.Contains(t, resp.Body.String(), models.LFSMetaFileIdentifier)
+		setting.CheckLFSVersion()
+		if setting.LFS.StartServer {
+			req = NewRequest(t, "GET", path.Join("/", username, reponame, "/raw/branch/master/", littleLFS))
+			resp = session.MakeRequest(t, req, http.StatusOK)
+			assert.NotEqual(t, littleSize, resp.Body.Len())
+			assert.Contains(t, resp.Body.String(), models.LFSMetaFileIdentifier)
+		}
 
 		if !testing.Short() {
 			req = NewRequest(t, "GET", path.Join("/", username, reponame, "/raw/branch/master/", big))
 			resp = session.MakeRequest(t, req, http.StatusOK)
 			assert.Equal(t, bigSize, resp.Body.Len())
 
-			req = NewRequest(t, "GET", path.Join("/", username, reponame, "/raw/branch/master/", bigLFS))
-			resp = session.MakeRequest(t, req, http.StatusOK)
-			assert.NotEqual(t, bigSize, resp.Body.Len())
-			assert.Contains(t, resp.Body.String(), models.LFSMetaFileIdentifier)
+			if setting.LFS.StartServer {
+				req = NewRequest(t, "GET", path.Join("/", username, reponame, "/raw/branch/master/", bigLFS))
+				resp = session.MakeRequest(t, req, http.StatusOK)
+				assert.NotEqual(t, bigSize, resp.Body.Len())
+				assert.Contains(t, resp.Body.String(), models.LFSMetaFileIdentifier)
+			}
 		}
 	})
 }
@@ -217,18 +243,23 @@ func mediaTest(t *testing.T, ctx *APITestContext, little, big, littleLFS, bigLFS
 		resp := session.MakeRequestNilResponseRecorder(t, req, http.StatusOK)
 		assert.Equal(t, littleSize, resp.Length)
 
-		req = NewRequest(t, "GET", path.Join("/", username, reponame, "/media/branch/master/", littleLFS))
-		resp = session.MakeRequestNilResponseRecorder(t, req, http.StatusOK)
-		assert.Equal(t, littleSize, resp.Length)
+		setting.CheckLFSVersion()
+		if setting.LFS.StartServer {
+			req = NewRequest(t, "GET", path.Join("/", username, reponame, "/media/branch/master/", littleLFS))
+			resp = session.MakeRequestNilResponseRecorder(t, req, http.StatusOK)
+			assert.Equal(t, littleSize, resp.Length)
+		}
 
 		if !testing.Short() {
 			req = NewRequest(t, "GET", path.Join("/", username, reponame, "/media/branch/master/", big))
 			resp = session.MakeRequestNilResponseRecorder(t, req, http.StatusOK)
 			assert.Equal(t, bigSize, resp.Length)
 
-			req = NewRequest(t, "GET", path.Join("/", username, reponame, "/media/branch/master/", bigLFS))
-			resp = session.MakeRequestNilResponseRecorder(t, req, http.StatusOK)
-			assert.Equal(t, bigSize, resp.Length)
+			if setting.LFS.StartServer {
+				req = NewRequest(t, "GET", path.Join("/", username, reponame, "/media/branch/master/", bigLFS))
+				resp = session.MakeRequestNilResponseRecorder(t, req, http.StatusOK)
+				assert.Equal(t, bigSize, resp.Length)
+			}
 		}
 	})
 }
@@ -274,6 +305,8 @@ func generateCommitWithNewData(size int, repoPath, email, fullName, prefix strin
 	}
 
 	//Commit
+	// Now here we should explicitly allow lfs filters to run
+	oldGlobals := allowLFSFilters()
 	err = git.AddChanges(repoPath, false, filepath.Base(tmpFile.Name()))
 	if err != nil {
 		return "", err
@@ -291,6 +324,7 @@ func generateCommitWithNewData(size int, repoPath, email, fullName, prefix strin
 		},
 		Message: fmt.Sprintf("Testing commit @ %v", time.Now()),
 	})
+	git.GlobalCommandArgs = oldGlobals
 	return filepath.Base(tmpFile.Name()), err
 }
 
diff --git a/integrations/lfs_getobject_test.go b/integrations/lfs_getobject_test.go
index 567cf13b45b..da3ddcec706 100644
--- a/integrations/lfs_getobject_test.go
+++ b/integrations/lfs_getobject_test.go
@@ -58,6 +58,11 @@ func storeObjectInRepo(t *testing.T, repositoryID int64, content *[]byte) string
 
 func doLfs(t *testing.T, content *[]byte, expectGzip bool) {
 	prepareTestEnv(t)
+	setting.CheckLFSVersion()
+	if !setting.LFS.StartServer {
+		t.Skip()
+		return
+	}
 	repo, err := models.GetRepositoryByOwnerAndName("user2", "repo1")
 	assert.NoError(t, err)
 	oid := storeObjectInRepo(t, repo.ID, content)
diff --git a/models/repo.go b/models/repo.go
index 976e8532325..36f27fef53a 100644
--- a/models/repo.go
+++ b/models/repo.go
@@ -1063,7 +1063,7 @@ func CleanUpMigrateInfo(repo *Repository) (*Repository, error) {
 		}
 	}
 
-	_, err := git.NewCommand("remote", "remove", "origin").RunInDir(repoPath)
+	_, err := git.NewCommand("remote", "rm", "origin").RunInDir(repoPath)
 	if err != nil && !strings.HasPrefix(err.Error(), "exit status 128 - fatal: No such remote ") {
 		return repo, fmt.Errorf("CleanUpMigrateInfo: %v", err)
 	}
diff --git a/models/repo_mirror.go b/models/repo_mirror.go
index c62834f6fb6..982672ea2b8 100644
--- a/models/repo_mirror.go
+++ b/models/repo_mirror.go
@@ -134,7 +134,7 @@ func (m *Mirror) FullAddress() string {
 func (m *Mirror) SaveAddress(addr string) error {
 	repoPath := m.Repo.RepoPath()
 	// Remove old origin
-	_, err := git.NewCommand("remote", "remove", "origin").RunInDir(repoPath)
+	_, err := git.NewCommand("remote", "rm", "origin").RunInDir(repoPath)
 	if err != nil && !strings.HasPrefix(err.Error(), "exit status 128 - fatal: No such remote ") {
 		return err
 	}
diff --git a/modules/git/repo_branch.go b/modules/git/repo_branch.go
index 9209f4a764f..3e1261d294c 100644
--- a/modules/git/repo_branch.go
+++ b/modules/git/repo_branch.go
@@ -165,7 +165,7 @@ func (repo *Repository) AddRemote(name, url string, fetch bool) error {
 
 // RemoveRemote removes a remote from repository.
 func (repo *Repository) RemoveRemote(name string) error {
-	_, err := NewCommand("remote", "remove", name).RunInDir(repo.Path)
+	_, err := NewCommand("remote", "rm", name).RunInDir(repo.Path)
 	return err
 }
 
diff --git a/modules/git/repo_tree.go b/modules/git/repo_tree.go
index f7c9dff923c..f6b393d8d86 100644
--- a/modules/git/repo_tree.go
+++ b/modules/git/repo_tree.go
@@ -6,11 +6,13 @@
 package git
 
 import (
+	"bytes"
 	"fmt"
 	"os"
 	"strings"
 	"time"
 
+	"github.com/mcuadros/go-version"
 	"gopkg.in/src-d/go-git.v4/plumbing"
 )
 
@@ -63,6 +65,11 @@ type CommitTreeOpts struct {
 
 // CommitTree creates a commit from a given tree id for the user with provided message
 func (repo *Repository) CommitTree(sig *Signature, tree *Tree, opts CommitTreeOpts) (SHA1, error) {
+	binVersion, err := BinVersion()
+	if err != nil {
+		return SHA1{}, err
+	}
+
 	commitTimeStr := time.Now().Format(time.RFC3339)
 
 	// Because this may call hooks we should pass in the environment
@@ -80,20 +87,24 @@ func (repo *Repository) CommitTree(sig *Signature, tree *Tree, opts CommitTreeOp
 		cmd.AddArguments("-p", parent)
 	}
 
-	cmd.AddArguments("-m", opts.Message)
+	messageBytes := new(bytes.Buffer)
+	_, _ = messageBytes.WriteString(opts.Message)
+	_, _ = messageBytes.WriteString("\n")
 
 	if opts.KeyID != "" {
 		cmd.AddArguments(fmt.Sprintf("-S%s", opts.KeyID))
 	}
 
-	if opts.NoGPGSign {
+	if version.Compare(binVersion, "2.0.0", ">=") && opts.NoGPGSign {
 		cmd.AddArguments("--no-gpg-sign")
 	}
 
-	res, err := cmd.RunInDirWithEnv(repo.Path, env)
+	stdout := new(bytes.Buffer)
+	stderr := new(bytes.Buffer)
+	err = cmd.RunInDirTimeoutEnvFullPipeline(env, -1, repo.Path, stdout, stderr, messageBytes)
 
 	if err != nil {
-		return SHA1{}, err
+		return SHA1{}, concatenateError(err, stderr.String())
 	}
-	return NewIDFromString(strings.TrimSpace(res))
+	return NewIDFromString(strings.TrimSpace(stdout.String()))
 }
diff --git a/modules/process/manager.go b/modules/process/manager.go
index 9ac3af86f10..3e77c0a6a90 100644
--- a/modules/process/manager.go
+++ b/modules/process/manager.go
@@ -1,4 +1,5 @@
 // Copyright 2014 The Gogs Authors. All rights reserved.
+// 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.
 
@@ -9,6 +10,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io"
 	"os/exec"
 	"sync"
 	"time"
@@ -93,6 +95,14 @@ func (pm *Manager) ExecDir(timeout time.Duration, dir, desc, cmdName string, arg
 // Returns its complete stdout and stderr
 // outputs and an error, if any (including timeout)
 func (pm *Manager) ExecDirEnv(timeout time.Duration, dir, desc string, env []string, cmdName string, args ...string) (string, string, error) {
+	return pm.ExecDirEnvStdIn(timeout, dir, desc, env, nil, cmdName, args...)
+}
+
+// ExecDirEnvStdIn runs a command in given path and environment variables with provided stdIN, and waits for its completion
+// up to the given timeout (or DefaultTimeout if -1 is given).
+// Returns its complete stdout and stderr
+// outputs and an error, if any (including timeout)
+func (pm *Manager) ExecDirEnvStdIn(timeout time.Duration, dir, desc string, env []string, stdIn io.Reader, cmdName string, args ...string) (string, string, error) {
 	if timeout == -1 {
 		timeout = 60 * time.Second
 	}
@@ -108,6 +118,10 @@ func (pm *Manager) ExecDirEnv(timeout time.Duration, dir, desc string, env []str
 	cmd.Env = env
 	cmd.Stdout = stdOut
 	cmd.Stderr = stdErr
+	if stdIn != nil {
+		cmd.Stdin = stdIn
+	}
+
 	if err := cmd.Start(); err != nil {
 		return "", "", err
 	}
diff --git a/modules/pull/merge.go b/modules/pull/merge.go
index 0e9e3b8b145..e9c77ff9d93 100644
--- a/modules/pull/merge.go
+++ b/modules/pull/merge.go
@@ -11,7 +11,6 @@ import (
 	"fmt"
 	"io/ioutil"
 	"os"
-	"path"
 	"path/filepath"
 	"strings"
 
@@ -22,6 +21,7 @@ import (
 	"code.gitea.io/gitea/modules/setting"
 	api "code.gitea.io/gitea/modules/structs"
 	"code.gitea.io/gitea/modules/util"
+	"github.com/mcuadros/go-version"
 )
 
 // Merge merges pull request to base repository.
@@ -66,20 +66,17 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 
 	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)
+	if err := git.InitRepository(tmpBasePath, false); err != nil {
+		return fmt.Errorf("git init: %v", err)
 	}
 
 	remoteRepoName := "head_repo"
+	baseBranch := "base"
 
 	// 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)
+		f, err := os.OpenFile(p, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0600)
 		if err != nil {
 			return err
 		}
@@ -91,25 +88,41 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 		return nil
 	}
 
-	if err := addCacheRepo(tmpBasePath, headRepoPath); err != nil {
+	if err := addCacheRepo(tmpBasePath, baseGitRepo.Path); err != nil {
 		return fmt.Errorf("addCacheRepo [%s -> %s]: %v", headRepoPath, tmpBasePath, err)
 	}
 
 	var errbuf strings.Builder
+	if err := git.NewCommand("remote", "add", "-t", pr.BaseBranch, "-m", pr.BaseBranch, "origin", baseGitRepo.Path).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git remote add [%s -> %s]: %s", baseGitRepo.Path, tmpBasePath, errbuf.String())
+	}
+
+	if err := git.NewCommand("fetch", "origin", "--no-tags", pr.BaseBranch+":"+baseBranch, pr.BaseBranch+":original_"+baseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git fetch [%s -> %s]: %s", headRepoPath, tmpBasePath, errbuf.String())
+	}
+
+	if err := git.NewCommand("symbolic-ref", "HEAD", git.BranchPrefix+baseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+		return fmt.Errorf("git symbolic-ref HEAD base [%s]: %s", tmpBasePath, errbuf.String())
+	}
+
+	if err := addCacheRepo(tmpBasePath, headRepoPath); err != nil {
+		return fmt.Errorf("addCacheRepo [%s -> %s]: %v", headRepoPath, tmpBasePath, err)
+	}
+
 	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())
 	}
 
+	trackingBranch := "tracking"
 	// Fetch head branch
-	if err := git.NewCommand("fetch", remoteRepoName, fmt.Sprintf("%s:refs/remotes/%s/%s", pr.HeadBranch, remoteRepoName, pr.HeadBranch)).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
+	if err := git.NewCommand("fetch", "--no-tags", remoteRepoName, pr.HeadBranch+":"+trackingBranch).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)
+	stagingBranch := "staging"
 
 	// Enable sparse-checkout
-	sparseCheckoutList, err := getDiffTree(tmpBasePath, pr.BaseBranch, trackingBranch)
+	sparseCheckoutList, err := getDiffTree(tmpBasePath, baseBranch, trackingBranch)
 	if err != nil {
 		return fmt.Errorf("getDiffTree: %v", err)
 	}
@@ -123,21 +136,37 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 		return fmt.Errorf("Writing sparse-checkout file to %s: %v", sparseCheckoutListPath, err)
 	}
 
+	gitConfigCommand := func() func() *git.Command {
+		binVersion, err := git.BinVersion()
+		if err != nil {
+			log.Fatal("Error retrieving git version: %v", err)
+		}
+
+		if version.Compare(binVersion, "1.8.0", ">=") {
+			return func() *git.Command {
+				return git.NewCommand("config", "--local")
+			}
+		}
+		return func() *git.Command {
+			return git.NewCommand("config")
+		}
+	}()
+
 	// 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 {
+	if err := gitConfigCommand().AddArguments("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 {
+	if err := gitConfigCommand().AddArguments("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 {
+	if err := gitConfigCommand().AddArguments("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 {
+	if err := gitConfigCommand().AddArguments("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 {
+	if err := gitConfigCommand().AddArguments("core.sparseCheckout", "true").RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
 		return fmt.Errorf("git config [core.sparsecheckout -> true]: %v", errbuf.String())
 	}
 
@@ -163,11 +192,11 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 			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 {
+		if err := git.NewCommand("rebase", "-q", 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 {
+		if err := git.NewCommand("checkout", baseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
 			return fmt.Errorf("git checkout: %s", errbuf.String())
 		}
 		// Merge fast forward
@@ -180,11 +209,11 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 			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 {
+		if err := git.NewCommand("rebase", "-q", 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 {
+		if err := git.NewCommand("checkout", baseBranch).RunInDirPipeline(tmpBasePath, nil, &errbuf); err != nil {
 			return fmt.Errorf("git checkout: %s", errbuf.String())
 		}
 		// Prepare merge with commit
@@ -216,7 +245,7 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 	if err != nil {
 		return fmt.Errorf("Failed to get full commit id for HEAD: %v", err)
 	}
-	mergeBaseSHA, err := git.GetFullCommitID(tmpBasePath, "origin/"+pr.BaseBranch)
+	mergeBaseSHA, err := git.GetFullCommitID(tmpBasePath, "original_"+baseBranch)
 	if err != nil {
 		return fmt.Errorf("Failed to get full commit id for origin/%s: %v", pr.BaseBranch, err)
 	}
@@ -249,7 +278,7 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 	)
 
 	// Push back to upstream.
-	if err := git.NewCommand("push", "origin", pr.BaseBranch).RunInDirTimeoutEnvPipeline(env, -1, tmpBasePath, nil, &errbuf); err != nil {
+	if err := git.NewCommand("push", "origin", baseBranch+":"+pr.BaseBranch).RunInDirTimeoutEnvPipeline(env, -1, tmpBasePath, nil, &errbuf); err != nil {
 		return fmt.Errorf("git push: %s", errbuf.String())
 	}
 
diff --git a/modules/repofiles/temp_repo.go b/modules/repofiles/temp_repo.go
index d640ba80b02..28f3836d0e1 100644
--- a/modules/repofiles/temp_repo.go
+++ b/modules/repofiles/temp_repo.go
@@ -20,6 +20,7 @@ import (
 	"code.gitea.io/gitea/modules/log"
 	"code.gitea.io/gitea/modules/process"
 	"code.gitea.io/gitea/modules/setting"
+	"github.com/mcuadros/go-version"
 )
 
 // TemporaryUploadRepository is a type to wrap our upload repositories as a shallow clone
@@ -253,6 +254,11 @@ func (t *TemporaryUploadRepository) CommitTree(author, committer *models.User, t
 	authorSig := author.NewGitSig()
 	committerSig := committer.NewGitSig()
 
+	binVersion, err := git.BinVersion()
+	if err != nil {
+		return "", fmt.Errorf("Unable to get git version: %v", err)
+	}
+
 	// FIXME: Should we add SSH_ORIGINAL_COMMAND to this
 	// Because this may call hooks we should pass in the environment
 	env := append(os.Environ(),
@@ -263,11 +269,21 @@ func (t *TemporaryUploadRepository) CommitTree(author, committer *models.User, t
 		"GIT_COMMITTER_EMAIL="+committerSig.Email,
 		"GIT_COMMITTER_DATE="+commitTimeStr,
 	)
-	commitHash, stderr, err := process.GetManager().ExecDirEnv(5*time.Minute,
+	messageBytes := new(bytes.Buffer)
+	_, _ = messageBytes.WriteString(message)
+	_, _ = messageBytes.WriteString("\n")
+
+	args := []string{"commit-tree", treeHash, "-p", "HEAD"}
+	if version.Compare(binVersion, "2.0.0", ">=") {
+		args = append(args, "--no-gpg-sign")
+	}
+
+	commitHash, stderr, err := process.GetManager().ExecDirEnvStdIn(5*time.Minute,
 		t.basePath,
 		fmt.Sprintf("commitTree (git commit-tree): %s", t.basePath),
 		env,
-		git.GitExecutable, "commit-tree", treeHash, "-p", "HEAD", "-m", message)
+		messageBytes,
+		git.GitExecutable, args...)
 	if err != nil {
 		return "", fmt.Errorf("git commit-tree: %s", stderr)
 	}
@@ -327,6 +343,12 @@ func (t *TemporaryUploadRepository) DiffIndex() (diff *models.Diff, err error) {
 
 // CheckAttribute checks the given attribute of the provided files
 func (t *TemporaryUploadRepository) CheckAttribute(attribute string, args ...string) (map[string]map[string]string, error) {
+	binVersion, err := git.BinVersion()
+	if err != nil {
+		log.Error("Error retrieving git version: %v", err)
+		return nil, err
+	}
+
 	stdOut := new(bytes.Buffer)
 	stdErr := new(bytes.Buffer)
 
@@ -334,7 +356,14 @@ func (t *TemporaryUploadRepository) CheckAttribute(attribute string, args ...str
 	ctx, cancel := context.WithTimeout(context.Background(), timeout)
 	defer cancel()
 
-	cmdArgs := []string{"check-attr", "-z", attribute, "--cached", "--"}
+	cmdArgs := []string{"check-attr", "-z", attribute}
+
+	// git check-attr --cached first appears in git 1.7.8
+	if version.Compare(binVersion, "1.7.8", ">=") {
+		cmdArgs = append(cmdArgs, "--cached")
+	}
+	cmdArgs = append(cmdArgs, "--")
+
 	for _, arg := range args {
 		if arg != "" {
 			cmdArgs = append(cmdArgs, arg)
@@ -352,7 +381,7 @@ func (t *TemporaryUploadRepository) CheckAttribute(attribute string, args ...str
 	}
 
 	pid := process.GetManager().Add(desc, cmd)
-	err := cmd.Wait()
+	err = cmd.Wait()
 	process.GetManager().Remove(pid)
 
 	if err != nil {
diff --git a/modules/repofiles/update.go b/modules/repofiles/update.go
index 47fe89cf630..4a8aeec638a 100644
--- a/modules/repofiles/update.go
+++ b/modules/repofiles/update.go
@@ -311,12 +311,6 @@ func CreateOrUpdateRepoFile(repo *models.Repository, doer *models.User, opts *Up
 		}
 	}
 
-	// Check there is no way this can return multiple infos
-	filename2attribute2info, err := t.CheckAttribute("filter", treePath)
-	if err != nil {
-		return nil, err
-	}
-
 	content := opts.Content
 	if bom {
 		content = string(base.UTF8BOM) + content
@@ -339,16 +333,23 @@ func CreateOrUpdateRepoFile(repo *models.Repository, doer *models.User, opts *Up
 	opts.Content = content
 	var lfsMetaObject *models.LFSMetaObject
 
-	if setting.LFS.StartServer && filename2attribute2info[treePath] != nil && filename2attribute2info[treePath]["filter"] == "lfs" {
-		// OK so we are supposed to LFS this data!
-		oid, err := models.GenerateLFSOid(strings.NewReader(opts.Content))
+	if setting.LFS.StartServer {
+		// Check there is no way this can return multiple infos
+		filename2attribute2info, err := t.CheckAttribute("filter", treePath)
 		if err != nil {
 			return nil, err
 		}
-		lfsMetaObject = &models.LFSMetaObject{Oid: oid, Size: int64(len(opts.Content)), RepositoryID: repo.ID}
-		content = lfsMetaObject.Pointer()
-	}
 
+		if filename2attribute2info[treePath] != nil && filename2attribute2info[treePath]["filter"] == "lfs" {
+			// OK so we are supposed to LFS this data!
+			oid, err := models.GenerateLFSOid(strings.NewReader(opts.Content))
+			if err != nil {
+				return nil, err
+			}
+			lfsMetaObject = &models.LFSMetaObject{Oid: oid, Size: int64(len(opts.Content)), RepositoryID: repo.ID}
+			content = lfsMetaObject.Pointer()
+		}
+	}
 	// Add the object to the database
 	objectHash, err := t.HashObject(strings.NewReader(content))
 	if err != nil {
diff --git a/modules/repofiles/upload.go b/modules/repofiles/upload.go
index f2ffec7ebcd..202e66b89a1 100644
--- a/modules/repofiles/upload.go
+++ b/modules/repofiles/upload.go
@@ -74,9 +74,12 @@ func UploadRepoFiles(repo *models.Repository, doer *models.User, opts *UploadRep
 		infos[i] = uploadInfo{upload: upload}
 	}
 
-	filename2attribute2info, err := t.CheckAttribute("filter", names...)
-	if err != nil {
-		return err
+	var filename2attribute2info map[string]map[string]string
+	if setting.LFS.StartServer {
+		filename2attribute2info, err = t.CheckAttribute("filter", names...)
+		if err != nil {
+			return err
+		}
 	}
 
 	// Copy uploaded files into repository.
@@ -88,7 +91,7 @@ func UploadRepoFiles(repo *models.Repository, doer *models.User, opts *UploadRep
 		defer file.Close()
 
 		var objectHash string
-		if filename2attribute2info[uploadInfo.upload.Name] != nil && filename2attribute2info[uploadInfo.upload.Name]["filter"] == "lfs" {
+		if setting.LFS.StartServer && filename2attribute2info[uploadInfo.upload.Name] != nil && filename2attribute2info[uploadInfo.upload.Name]["filter"] == "lfs" {
 			// Handle LFS
 			// FIXME: Inefficient! this should probably happen in models.Upload
 			oid, err := models.GenerateLFSOid(file)