From 444959540a32f944100144d280acdcf12ed3f3f4b1ce8ec658f3bee3abd7ba4a Mon Sep 17 00:00:00 2001
From: Adam Majer <amajer@suse.com>
Date: Mon, 1 Sep 2025 16:39:13 +0200
Subject: [PATCH 1/3] submodule conflict resolution

If merging a ProjectGit with submodules,
  * removed submodules are to be removed always
  * modified/added submodules are to be present
  * submodules modified in base project and PR should conflict
---
 common/git_parser.go      | 296 +++++++++++++++++++++++++++++++++++
 common/git_utils.go       | 320 ++++++++++++++++----------------------
 common/git_utils_test.go  | 149 +++++++++++++++++-
 common/pr.go              |  78 +---------
 common/pr_test.go         |  34 ++--
 common/test_repo_setup.sh |  20 ++-
 6 files changed, 610 insertions(+), 287 deletions(-)
 create mode 100644 common/git_parser.go

diff --git a/common/git_parser.go b/common/git_parser.go
new file mode 100644
index 0000000..91f3658
--- /dev/null
+++ b/common/git_parser.go
@@ -0,0 +1,296 @@
+package common
+
+import (
+	"errors"
+	"fmt"
+	"io"
+)
+
+const (
+	GitStatus_Untracked = 0
+	GitStatus_Modified  = 1
+	GitStatus_Ignored   = 2
+	GitStatus_Unmerged  = 3 // States[0..3] -- Stage1, Stage2, Stage3 of merge objects
+	GitStatus_Renamed   = 4 // orig name in States[0]
+)
+
+type GitStatusData struct {
+	Path   string
+	Status int
+	States [3]string
+
+	/*
+	 <sub> A 4 character field describing the submodule state.
+	            "N..." when the entry is not a submodule.
+	            "S<c><m><u>" when the entry is a submodule.
+	            <c> is "C" if the commit changed; otherwise ".".
+	            <m> is "M" if it has tracked changes; otherwise ".".
+	            <u> is "U" if there are untracked changes; otherwise ".".
+	*/
+	SubmoduleChanges string
+}
+
+func parseGit_HexString(data io.ByteReader) (string, error) {
+	str := make([]byte, 0, 32)
+	for {
+		c, err := data.ReadByte()
+		if err != nil {
+			return "", err
+		}
+		switch {
+		case c == 0 || c == ' ':
+			return string(str), nil
+		case c >= 'a' && c <= 'f':
+		case c >= 'A' && c <= 'F':
+		case c >= '0' && c <= '9':
+		default:
+			return "", errors.New("Invalid character in hex string:" + string(c))
+		}
+		str = append(str, c)
+	}
+}
+func parseGit_String(data io.ByteReader) (string, error) {
+	str := make([]byte, 0, 100)
+	for {
+		c, err := data.ReadByte()
+		if err != nil {
+			return "", errors.New("Unexpected EOF. Expected NUL string term")
+		}
+		if c == 0 || c == ' ' {
+			return string(str), nil
+		}
+		str = append(str, c)
+	}
+}
+
+func parseGit_StringWithSpace(data io.ByteReader) (string, error) {
+	str := make([]byte, 0, 100)
+	for {
+		c, err := data.ReadByte()
+		if err != nil {
+			return "", errors.New("Unexpected EOF. Expected NUL string term")
+		}
+		if c == 0 {
+			return string(str), nil
+		}
+		str = append(str, c)
+	}
+}
+
+func skipGitStatusEntry(data io.ByteReader, skipSpaceLen int) error {
+	for skipSpaceLen > 0 {
+		c, err := data.ReadByte()
+		if err != nil {
+			return err
+		}
+		if c == ' ' {
+			skipSpaceLen--
+		}
+	}
+
+	return nil
+}
+
+func parseSingleStatusEntry(data io.ByteReader) (*GitStatusData, error) {
+	ret := GitStatusData{}
+	statusType, err := data.ReadByte()
+	if err != nil {
+		return nil, nil
+	}
+	switch statusType {
+	case '1':
+		var err error
+		if err = skipGitStatusEntry(data, 8); err != nil {
+			return nil, err
+		}
+		ret.Status = GitStatus_Modified
+		ret.Path, err = parseGit_StringWithSpace(data)
+		if err != nil {
+			return nil, err
+		}
+	case '2':
+		var err error
+		if err = skipGitStatusEntry(data, 9); err != nil {
+			return nil, err
+		}
+		ret.Status = GitStatus_Renamed
+		ret.Path, err = parseGit_StringWithSpace(data)
+		if err != nil {
+			return nil, err
+		}
+		ret.States[0], err = parseGit_StringWithSpace(data)
+		if err != nil {
+			return nil, err
+		}
+	case '?':
+		var err error
+		if err = skipGitStatusEntry(data, 1); err != nil {
+			return nil, err
+		}
+		ret.Status = GitStatus_Untracked
+		ret.Path, err = parseGit_StringWithSpace(data)
+		if err != nil {
+			return nil, err
+		}
+	case '!':
+		var err error
+		if err = skipGitStatusEntry(data, 1); err != nil {
+			return nil, err
+		}
+		ret.Status = GitStatus_Ignored
+		ret.Path, err = parseGit_StringWithSpace(data)
+		if err != nil {
+			return nil, err
+		}
+	case 'u':
+		var err error
+		if err = skipGitStatusEntry(data, 2); err != nil {
+			return nil, err
+		}
+		if ret.SubmoduleChanges, err = parseGit_String(data); err != nil {
+			return nil, err
+		}
+		if err = skipGitStatusEntry(data, 4); err != nil {
+			return nil, err
+		}
+
+		if ret.States[0], err = parseGit_HexString(data); err != nil {
+			return nil, err
+		}
+		if ret.States[1], err = parseGit_HexString(data); err != nil {
+			return nil, err
+		}
+		if ret.States[2], err = parseGit_HexString(data); err != nil {
+			return nil, err
+		}
+		ret.Status = GitStatus_Unmerged
+		ret.Path, err = parseGit_StringWithSpace(data)
+		if err != nil {
+			return nil, err
+		}
+	default:
+		return nil, errors.New("Invalid status type" + string(statusType))
+	}
+	return &ret, nil
+}
+
+func parseGitStatusData(data io.ByteReader) (Data, error) {
+	ret := make([]GitStatusData, 0, 10)
+	for {
+		data, err := parseSingleStatusEntry(data)
+		if err != nil {
+			return nil, err
+		} else if data == nil {
+			break
+		}
+
+		ret = append(ret, *data)
+	}
+	return ret, nil
+}
+
+type Data interface{}
+
+type CommitStatus int
+
+const (
+	Add CommitStatus = iota
+	Rm
+	Copy
+	Modify
+	Rename
+	TypeChange
+	Unmerged
+	Unknown
+)
+
+type GitDiffRawData struct {
+	SrcMode, DstMode     string
+	SrcCommit, DstCommit string
+	Status               CommitStatus
+	Src, Dst             string
+}
+
+func parseGit_DiffIndexStatus(data io.ByteReader, d *GitDiffRawData) error {
+	b, err := data.ReadByte()
+	if err != nil {
+		return err
+	}
+
+	switch b {
+	case 'A':
+		d.Status = Add
+	case 'C':
+		d.Status = Copy
+	case 'D':
+		d.Status = Rm
+	case 'M':
+		d.Status = Modify
+	case 'R':
+		d.Status = Rename
+	case 'T':
+		d.Status = TypeChange
+	case 'U':
+		d.Status = Unmerged
+	case 'X':
+		return fmt.Errorf("Unexpected unknown change type. This is a git bug")
+	}
+	_, err = parseGit_StringWithSpace(data)
+	if err != nil {
+		return err
+	}
+
+	return nil
+}
+
+func parseSingleGitDiffIndexRawData(data io.ByteReader) (*GitDiffRawData, error) {
+	var ret GitDiffRawData
+
+	b, err := data.ReadByte()
+	if err != nil {
+		return nil, err
+	}
+	if b != ':' {
+		return nil, fmt.Errorf("Expected ':' but got '%s'", string(b))
+	}
+
+	if ret.SrcMode, err = parseGit_String(data); err != nil {
+		return nil, err
+	}
+	if ret.DstMode, err = parseGit_String(data); err != nil {
+		return nil, err
+	}
+	if ret.Src, err = parseGit_String(data); err != nil {
+		return nil, err
+	}
+	if ret.Dst, err = parseGit_String(data); err != nil {
+		return nil, err
+	}
+	if err = parseGit_DiffIndexStatus(data, &ret); err != nil {
+		return nil, err
+	}
+	ret.Dst = ret.Src
+	switch ret.Status {
+	case Copy, Rename:
+		if ret.Src, err = parseGit_StringWithSpace(data); err != nil {
+			return nil, err
+		}
+	}
+
+	return &ret, nil
+}
+
+func parseGitDiffIndexRawData(data io.ByteReader) (Data, error) {
+	ret := make([]GitDiffRawData, 0, 10)
+	for {
+		data, err := parseSingleGitDiffIndexRawData(data)
+		if err != nil {
+			return nil, err
+		} else if data == nil {
+			break
+		}
+
+		ret = append(ret, *data)
+	}
+	return ret, nil
+}
diff --git a/common/git_utils.go b/common/git_utils.go
index bd5342a..47c64c3 100644
--- a/common/git_utils.go
+++ b/common/git_utils.go
@@ -19,9 +19,7 @@ package common
  */
 
 import (
-	"bufio"
 	"bytes"
-	"errors"
 	"fmt"
 	"io"
 	"os"
@@ -44,6 +42,10 @@ type GitDirectoryLister interface {
 	GitDirectoryList(gitPath, commitId string) (dirlist map[string]string, err error)
 }
 
+type GitSubmoduleFileConflictResolver interface {
+	GitResolveSubmoduleFileConflict(cwd, MergeBase, Head, MergeHead string) error
+}
+
 type GitStatusLister interface {
 	GitStatus(cwd string) ([]GitStatusData, error)
 }
@@ -75,6 +77,7 @@ type Git interface {
 	GitExecQuietOrPanic(cwd string, params ...string)
 
 	GitDiffLister
+	GitSubmoduleFileConflictResolver
 }
 
 type GitHandlerImpl struct {
@@ -1002,193 +1005,10 @@ func (e *GitHandlerImpl) GitSubmoduleCommitId(cwd, packageName, commitId string)
 	return subCommitId, len(subCommitId) > 0
 }
 
-const (
-	GitStatus_Untracked = 0
-	GitStatus_Modified  = 1
-	GitStatus_Ignored   = 2
-	GitStatus_Unmerged  = 3 // States[0..3] -- Stage1, Stage2, Stage3 of merge objects
-	GitStatus_Renamed   = 4 // orig name in States[0]
-)
-
-type GitStatusData struct {
-	Path   string
-	Status int
-	States [3]string
-
-	/*
-	 <sub> A 4 character field describing the submodule state.
-	            "N..." when the entry is not a submodule.
-	            "S<c><m><u>" when the entry is a submodule.
-	            <c> is "C" if the commit changed; otherwise ".".
-	            <m> is "M" if it has tracked changes; otherwise ".".
-	            <u> is "U" if there are untracked changes; otherwise ".".
-	*/
-	SubmoduleChanges string
-}
-
-func parseGitStatusHexString(data io.ByteReader) (string, error) {
-	str := make([]byte, 0, 32)
-	for {
-		c, err := data.ReadByte()
-		if err != nil {
-			return "", err
-		}
-		switch {
-		case c == 0 || c == ' ':
-			return string(str), nil
-		case c >= 'a' && c <= 'f':
-		case c >= 'A' && c <= 'F':
-		case c >= '0' && c <= '9':
-		default:
-			return "", errors.New("Invalid character in hex string:" + string(c))
-		}
-		str = append(str, c)
-	}
-}
-func parseGitStatusString(data io.ByteReader) (string, error) {
-	str := make([]byte, 0, 100)
-	for {
-		c, err := data.ReadByte()
-		if err != nil {
-			return "", errors.New("Unexpected EOF. Expected NUL string term")
-		}
-		if c == 0 || c == ' ' {
-			return string(str), nil
-		}
-		str = append(str, c)
-	}
-}
-
-func parseGitStatusStringWithSpace(data io.ByteReader) (string, error) {
-	str := make([]byte, 0, 100)
-	for {
-		c, err := data.ReadByte()
-		if err != nil {
-			return "", errors.New("Unexpected EOF. Expected NUL string term")
-		}
-		if c == 0 {
-			return string(str), nil
-		}
-		str = append(str, c)
-	}
-}
-
-func skipGitStatusEntry(data io.ByteReader, skipSpaceLen int) error {
-	for skipSpaceLen > 0 {
-		c, err := data.ReadByte()
-		if err != nil {
-			return err
-		}
-		if c == ' ' {
-			skipSpaceLen--
-		}
-	}
-
-	return nil
-}
-
-func parseSingleStatusEntry(data io.ByteReader) (*GitStatusData, error) {
-	ret := GitStatusData{}
-	statusType, err := data.ReadByte()
-	if err != nil {
-		return nil, nil
-	}
-	switch statusType {
-	case '1':
-		var err error
-		if err = skipGitStatusEntry(data, 8); err != nil {
-			return nil, err
-		}
-		ret.Status = GitStatus_Modified
-		ret.Path, err = parseGitStatusStringWithSpace(data)
-		if err != nil {
-			return nil, err
-		}
-	case '2':
-		var err error
-		if err = skipGitStatusEntry(data, 9); err != nil {
-			return nil, err
-		}
-		ret.Status = GitStatus_Renamed
-		ret.Path, err = parseGitStatusStringWithSpace(data)
-		if err != nil {
-			return nil, err
-		}
-		ret.States[0], err = parseGitStatusStringWithSpace(data)
-		if err != nil {
-			return nil, err
-		}
-	case '?':
-		var err error
-		if err = skipGitStatusEntry(data, 1); err != nil {
-			return nil, err
-		}
-		ret.Status = GitStatus_Untracked
-		ret.Path, err = parseGitStatusStringWithSpace(data)
-		if err != nil {
-			return nil, err
-		}
-	case '!':
-		var err error
-		if err = skipGitStatusEntry(data, 1); err != nil {
-			return nil, err
-		}
-		ret.Status = GitStatus_Ignored
-		ret.Path, err = parseGitStatusStringWithSpace(data)
-		if err != nil {
-			return nil, err
-		}
-	case 'u':
-		var err error
-		if err = skipGitStatusEntry(data, 2); err != nil {
-			return nil, err
-		}
-		if ret.SubmoduleChanges, err = parseGitStatusString(data); err != nil {
-			return nil, err
-		}
-		if err = skipGitStatusEntry(data, 4); err != nil {
-			return nil, err
-		}
-
-		if ret.States[0], err = parseGitStatusHexString(data); err != nil {
-			return nil, err
-		}
-		if ret.States[1], err = parseGitStatusHexString(data); err != nil {
-			return nil, err
-		}
-		if ret.States[2], err = parseGitStatusHexString(data); err != nil {
-			return nil, err
-		}
-		ret.Status = GitStatus_Unmerged
-		ret.Path, err = parseGitStatusStringWithSpace(data)
-		if err != nil {
-			return nil, err
-		}
-	default:
-		return nil, errors.New("Invalid status type" + string(statusType))
-	}
-	return &ret, nil
-}
-
-func parseGitStatusData(data io.ByteReader) ([]GitStatusData, error) {
-	ret := make([]GitStatusData, 0, 10)
-	for {
-		data, err := parseSingleStatusEntry(data)
-		if err != nil {
-			return nil, err
-		} else if data == nil {
-			break
-		}
-
-		ret = append(ret, *data)
-	}
-	return ret, nil
-}
-
-func (e *GitHandlerImpl) GitStatus(cwd string) (ret []GitStatusData, err error) {
-	LogDebug("getting git-status()")
-
-	cmd := exec.Command("/usr/bin/git", "status", "--porcelain=2", "-z")
+func (e *GitHandlerImpl) GitExecWithDataParse(cwd string, dataprocessor func(io.ByteReader) (Data, error), gitcmd string, args ...string) (Data, error) {
+	LogDebug("getting", gitcmd)
+	args = append([]string{gitcmd}, args...)
+	cmd := exec.Command("/usr/bin/git", args...)
 	cmd.Env = []string{
 		"GIT_CEILING_DIRECTORIES=" + e.GitPath,
 		"GIT_LFS_SKIP_SMUDGE=1",
@@ -1205,7 +1025,12 @@ func (e *GitHandlerImpl) GitStatus(cwd string) (ret []GitStatusData, err error)
 		LogError("Error running command", cmd.Args, err)
 	}
 
-	return parseGitStatusData(bufio.NewReader(bytes.NewReader(out)))
+	return dataprocessor(bytes.NewReader(out))
+}
+
+func (e *GitHandlerImpl) GitStatus(cwd string) (ret []GitStatusData, err error) {
+	data, err := e.GitExecWithDataParse(cwd, parseGitStatusData, "status", "--porcelain=2", "-z")
+	return data.([]GitStatusData), err
 }
 
 func (e *GitHandlerImpl) GitDiff(cwd, base, head string) (string, error) {
@@ -1230,3 +1055,118 @@ func (e *GitHandlerImpl) GitDiff(cwd, base, head string) (string, error) {
 
 	return string(out), nil
 }
+
+func (e *GitHandlerImpl) GitDiffIndex(cwd, commit string) ([]GitDiffRawData, error) {
+	data, err := e.GitExecWithDataParse("diff-index", parseGitDiffIndexRawData, cwd, "diff-index", "-z", "--raw", "--full-index", "--submodule=short", "HEAD")
+	return data.([]GitDiffRawData), err
+}
+
+func (git *GitHandlerImpl) GitResolveSubmoduleFileConflict(cwd, mergeBase, head, mergeHead string) error {
+	status, err := git.GitStatus(cwd)
+	if err != nil {
+		return fmt.Errorf("Status failed: %w", err)
+	}
+
+	// we can only resolve conflicts with .gitmodules
+	for _, s := range status {
+		if s.Status == GitStatus_Unmerged {
+			if s.Path != ".gitmodules" {
+				return fmt.Errorf("Conflict elsewhere than submodules: %s", s.Path)
+			}
+
+			submodules1, err := git.GitSubmoduleList(cwd, mergeBase)
+			if err != nil {
+				return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
+			}
+/*
+			submodules2, err := git.GitSubmoduleList(cwd, head)
+			if err != nil {
+				return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
+			}
+*/
+			submodules3, err := git.GitSubmoduleList(cwd, mergeHead)
+			if err != nil {
+				return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
+			}
+
+			// find modified submodules in the mergeHead
+			modifiedSubmodules := make([]string, 0, 10)
+			removedSubmodules := make([]string, 0, 10)
+			addedSubmodules := make([]string, 0, 10)
+
+			for submodulePath, oldHash := range submodules1 {
+				if newHash, found := submodules3[submodulePath]; found && newHash != oldHash {
+					modifiedSubmodules = append(modifiedSubmodules, submodulePath)
+				} else if !found {
+					removedSubmodules = append(removedSubmodules, submodulePath)
+				}
+			}
+			for submodulePath, _ := range submodules3 {
+				if _, found := submodules1[submodulePath]; !found {
+					addedSubmodules = append(addedSubmodules, submodulePath)
+				}
+			}
+
+			// We need to adjust the `submodules` list by the pending changes to the index
+			s1, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[0])
+			if err != nil {
+				return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
+			}
+			s2, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[1])
+			if err != nil {
+				return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
+			}
+			s3, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[2])
+			if err != nil {
+				return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
+			}
+
+			_, err = ParseSubmodulesFile(strings.NewReader(s1))
+			if err != nil {
+				return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
+			}
+			subs2, err := ParseSubmodulesFile(strings.NewReader(s2))
+			if err != nil {
+				return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
+			}
+			subs3, err := ParseSubmodulesFile(strings.NewReader(s3))
+			if err != nil {
+				return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
+			}
+
+			overrideSet := make([]Submodule, 0, len(addedSubmodules)+len(modifiedSubmodules))
+			for i := range subs3 {
+				if slices.Contains(addedSubmodules, subs3[i].Path) || slices.Contains(modifiedSubmodules, subs3[i].Path) {
+					overrideSet = append(overrideSet, subs3[i])
+				}
+			}
+			// merge from subs1 (merge-base), subs2 (changes in base since merge-base HEAD), subs3 (merge_source MERGE_HEAD)
+			// this will update submodules
+			SubmoduleCompare := func(a, b Submodule) int { return strings.Compare(a.Path, b.Path) }
+			CompactCompare := func(a, b Submodule) bool { return a.Path == b.Path }
+
+			// remove submodules that are removed in the PR
+			subs2 = slices.DeleteFunc(subs2, func(a Submodule) bool { return slices.Contains(removedSubmodules, a.Path) })
+
+			mergedSubs := slices.Concat(overrideSet, subs2)
+			slices.SortStableFunc(mergedSubs, SubmoduleCompare)
+			filteredSubs := slices.CompactFunc(mergedSubs, CompactCompare)
+
+			out, err := os.Create(path.Join(git.GetPath(), cwd, ".gitmodules"))
+			if err != nil {
+				return fmt.Errorf("Can't open .gitmodules for writing: %w", err)
+			}
+			if err = WriteSubmodules(filteredSubs, out); err != nil {
+				return fmt.Errorf("Can't write .gitmodules: %w", err)
+			}
+			if out.Close(); err != nil {
+				return fmt.Errorf("Can't close .gitmodules: %w", err)
+			}
+
+			git.GitExecOrPanic(cwd, "add", ".gitmodules")
+			git.GitExecOrPanic(cwd, "-c", "core.editor=true", "merge", "--continue")
+		}
+	}
+
+	return nil
+}
diff --git a/common/git_utils_test.go b/common/git_utils_test.go
index 342b3b4..d3befdf 100644
--- a/common/git_utils_test.go
+++ b/common/git_utils_test.go
@@ -24,6 +24,7 @@ import (
 	"os"
 	"os/exec"
 	"path"
+	"runtime/debug"
 	"slices"
 	"strings"
 	"testing"
@@ -93,6 +94,145 @@ func TestGitClone(t *testing.T) {
 	}
 }
 
+func TestSubmoduleConflictResolution(t *testing.T) {
+	tests := []struct {
+		name            string
+		checkout, merge string
+		result          string
+		merge_fail      bool
+	}{
+		{
+			name:     "adding two submodules",
+			checkout: "base_add_b1",
+			merge:    "base_add_b2",
+			result: `[submodule "pkgA"]
+	path = pkgA
+	url = ../pkgA
+[submodule "pkgB"]
+	path = pkgB
+	url = ../pkgB
+[submodule "pkgB1"]
+	path = pkgB1
+	url = ../pkgB1
+[submodule "pkgB2"]
+	path = pkgB2
+	url = ../pkgB2
+[submodule "pkgC"]
+	path = pkgC
+	url = ../pkgC
+`,
+		},
+		{
+			name:     "remove one module and add another",
+			checkout: "base_rm_c",
+			merge:    "base_add_b2",
+			result: `[submodule "pkgA"]
+	path = pkgA
+	url = ../pkgA
+[submodule "pkgB"]
+	path = pkgB
+	url = ../pkgB
+[submodule "pkgB2"]
+	path = pkgB2
+	url = ../pkgB2
+`,
+		},
+		{
+			name:     "add one and remove another",
+			checkout: "base_add_b2",
+			merge:    "base_rm_c",
+			result: `[submodule "pkgA"]
+	path = pkgA
+	url = ../pkgA
+[submodule "pkgB"]
+	path = pkgB
+	url = ../pkgB
+[submodule "pkgB2"]
+	path = pkgB2
+	url = ../pkgB2
+`,
+		},
+		{
+			name:       "rm modified submodule",
+			checkout:   "base_modify_c",
+			merge:      "base_rm_c",
+			merge_fail: true,
+		},
+		{
+			name:       "modified removed submodule",
+			checkout:   "base_rm_c",
+			merge:      "base_modify_c",
+			merge_fail: true,
+		},
+	}
+
+	d, err := os.MkdirTemp(os.TempDir(), "submoduletests")
+	if err != nil {
+		t.Fatal(err)
+	}
+	cwd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	cmd := exec.Command(cwd + "/test_repo_setup.sh")
+	cmd.Dir = d
+	_, err = cmd.Output()
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	gh, err := AllocateGitWorkTree(d, "test", "foo@example.com")
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	success := true
+	noErrorOrFail := func(t *testing.T, err error) {
+		if err != nil {
+			t.Fatal(string(debug.Stack()), err)
+		}
+	}
+	for _, test := range tests {
+		success = t.Run(test.name, func(t *testing.T) {
+			git, err := gh.ReadExistingPath("prjgit")
+			defer git.Close()
+
+			if err != nil {
+				t.Fatal(err)
+			}
+			noErrorOrFail(t, git.GitExec("", "reset", "--hard"))
+			noErrorOrFail(t, git.GitExec("", "checkout", "-B", "test", test.checkout))
+			//			noErrorOrFail(t, git.GitExec("", "merge", test.checkout))
+			err = git.GitExec("", "merge", test.merge)
+			if err == nil {
+				t.Fatal("expected a conflict")
+			}
+			err = git.GitResolveSubmoduleFileConflict("", "main", test.checkout, test.merge)
+			if err != nil {
+				if test.merge_fail {
+					return // success
+				}
+				t.Fatal(err)
+			}
+			if test.merge_fail {
+				t.Fatal("Expected fail but succeeded?")
+			}
+			data, err := os.ReadFile(git.GetPath() + "/.gitmodules")
+			if err != nil {
+				t.Fatal("Cannot read .gitmodules.", err)
+			}
+
+			if string(data) != test.result {
+				t.Error("Expected", len(test.result), test.result, "but have", len(data), string(data))
+			}
+		}) && success
+	}
+
+	if success {
+		os.RemoveAll(d)
+	}
+}
+
 func TestGitMsgParsing(t *testing.T) {
 	t.Run("tree message with size 56", func(t *testing.T) {
 		const hdr = "f40888ea4515fe2e8eea617a16f5f50a45f652d894de3ad181d58de3aafb8f98 tree 56\x00"
@@ -584,12 +724,15 @@ func TestGitStatusParse(t *testing.T) {
 			if err != nil {
 				t.Fatal(err)
 			}
-			if len(r) != len(test.res) {
-				t.Fatal("len(r):", len(r), "is not expected", len(test.res))
+
+			res := r.([]GitStatusData)
+
+			if len(res) != len(test.res) {
+				t.Fatal("len(r):", len(res), "is not expected", len(test.res))
 			}
 
 			for _, expected := range test.res {
-				if !slices.Contains(r, expected) {
+				if !slices.Contains(res, expected) {
 					t.Fatal("result", r, "doesn't contains expected", expected)
 				}
 			}
diff --git a/common/pr.go b/common/pr.go
index 5cd11f9..e5a7aa3 100644
--- a/common/pr.go
+++ b/common/pr.go
@@ -4,8 +4,6 @@ import (
 	"bufio"
 	"errors"
 	"fmt"
-	"os"
-	"path"
 	"slices"
 	"strings"
 
@@ -433,80 +431,8 @@ func (rs *PRSet) Merge(gitea GiteaReviewUnrequester, git Git) error {
 
 	err = git.GitExec(DefaultGitPrj, "merge", "--no-ff", "-m", msg, prjgit.Head.Sha)
 	if err != nil {
-		status, statusErr := git.GitStatus(DefaultGitPrj)
-		if statusErr != nil {
-			return fmt.Errorf("Failed to merge: %w . Status also failed: %w", err, statusErr)
-		}
-
-		// we can only resolve conflicts with .gitmodules
-		for _, s := range status {
-			if s.Status == GitStatus_Unmerged {
-				panic("Can't handle conflicts yet")
-				if s.Path != ".gitmodules" {
-					return err
-				}
-
-				submodules, err := git.GitSubmoduleList(DefaultGitPrj, "MERGE_HEAD")
-				if err != nil {
-					return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
-				}
-				s1, err := git.GitExecWithOutput(DefaultGitPrj, "cat-file", "blob", s.States[0])
-				if err != nil {
-					return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
-				}
-				s2, err := git.GitExecWithOutput(DefaultGitPrj, "cat-file", "blob", s.States[1])
-				if err != nil {
-					return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
-				}
-				s3, err := git.GitExecWithOutput(DefaultGitPrj, "cat-file", "blob", s.States[2])
-				if err != nil {
-					return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
-				}
-
-				subs1, err := ParseSubmodulesFile(strings.NewReader(s1))
-				if err != nil {
-					return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
-				}
-				subs2, err := ParseSubmodulesFile(strings.NewReader(s2))
-				if err != nil {
-					return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
-				}
-				subs3, err := ParseSubmodulesFile(strings.NewReader(s3))
-				if err != nil {
-					return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
-				}
-
-				// merge from subs3 (target), subs1 (orig), subs2 (2-nd base that is missing from target base)
-				// this will update submodules
-				mergedSubs := slices.Concat(subs1, subs2, subs3)
-
-				var filteredSubs []Submodule = make([]Submodule, 0, max(len(subs1), len(subs2), len(subs3)))
-			nextSub:
-				for subName := range submodules {
-
-					for i := range mergedSubs {
-						if path.Base(mergedSubs[i].Path) == subName {
-							filteredSubs = append(filteredSubs, mergedSubs[i])
-							continue nextSub
-						}
-					}
-					return fmt.Errorf("Cannot find submodule for path: %s", subName)
-				}
-
-				out, err := os.Create(path.Join(git.GetPath(), DefaultGitPrj, ".gitmodules"))
-				if err != nil {
-					return fmt.Errorf("Can't open .gitmodules for writing: %w", err)
-				}
-				if err = WriteSubmodules(filteredSubs, out); err != nil {
-					return fmt.Errorf("Can't write .gitmodules: %w", err)
-				}
-				if out.Close(); err != nil {
-					return fmt.Errorf("Can't close .gitmodules: %w", err)
-				}
-
-				git.GitExecOrPanic(DefaultGitPrj, "add", ".gitmodules")
-				git.GitExecOrPanic(DefaultGitPrj, "-c", "core.editor=true", "merge", "--continue")
-			}
+		if resolveError := git.GitResolveSubmoduleFileConflict(DefaultGitPrj, prjgit.MergeBase, prjgit.Base.Sha, prjgit.Head.Sha); resolveError != nil {
+			return fmt.Errorf("Merge failed. (%w): %w", err, resolveError)
 		}
 	}
 
diff --git a/common/pr_test.go b/common/pr_test.go
index c59dde3..3fadb2e 100644
--- a/common/pr_test.go
+++ b/common/pr_test.go
@@ -15,22 +15,23 @@ import (
 	"src.opensuse.org/autogits/common/gitea-generated/models"
 	mock_common "src.opensuse.org/autogits/common/mock"
 )
-/*
-func TestCockpit(t *testing.T) {
-	common.SetLoggingLevel(common.LogLevelDebug)
-	gitea := common.AllocateGiteaTransport("https://src.opensuse.org")
-	tl, err := gitea.GetTimeline("cockpit", "cockpit", 29)
-	if err != nil {
-		t.Fatal("Fail to timeline", err)
-	}
-	t.Log(tl)
-	r, err := common.FetchGiteaReviews(gitea, []string{}, "cockpit", "cockpit", 29)
-	if err != nil {
-		t.Fatal("Error:", err)
-	}
 
-	t.Error(r)
-}
+/*
+	func TestCockpit(t *testing.T) {
+		common.SetLoggingLevel(common.LogLevelDebug)
+		gitea := common.AllocateGiteaTransport("https://src.opensuse.org")
+		tl, err := gitea.GetTimeline("cockpit", "cockpit", 29)
+		if err != nil {
+			t.Fatal("Fail to timeline", err)
+		}
+		t.Log(tl)
+		r, err := common.FetchGiteaReviews(gitea, []string{}, "cockpit", "cockpit", 29)
+		if err != nil {
+			t.Fatal("Error:", err)
+		}
+
+		t.Error(r)
+	}
 */
 func reviewsToTimeline(reviews []*models.PullReview) []*models.TimelineComment {
 	timeline := make([]*models.TimelineComment, len(reviews))
@@ -940,6 +941,7 @@ func TestPRMerge(t *testing.T) {
 			pr: &models.PullRequest{
 				Base: &models.PRBranchInfo{
 					Sha: "e8b0de43d757c96a9d2c7101f4bff404e322f53a1fa4041fb85d646110c38ad4", // "base_add_b1"
+					Name: "master",
 					Repo: &models.Repository{
 						Name: "prj",
 						Owner: &models.User{
@@ -960,6 +962,7 @@ func TestPRMerge(t *testing.T) {
 			pr: &models.PullRequest{
 				Base: &models.PRBranchInfo{
 					Sha: "4fbd1026b2d7462ebe9229a49100c11f1ad6555520a21ba515122d8bc41328a8",
+					Name: "master",
 					Repo: &models.Repository{
 						Name: "prj",
 						Owner: &models.User{
@@ -979,6 +982,7 @@ func TestPRMerge(t *testing.T) {
 		t.Run(test.name, func(t *testing.T) {
 			ctl := gomock.NewController(t)
 			mock := mock_common.NewMockGiteaPRTimelineFetcher(ctl)
+
 			reviewUnrequestMock := mock_common.NewMockGiteaReviewUnrequester(ctl)
 
 			reviewUnrequestMock.EXPECT().UnrequestReview(gomock.Any(), gomock.Any(), gomock.Any(), gomock.Any()).Return(nil)
diff --git a/common/test_repo_setup.sh b/common/test_repo_setup.sh
index be58c22..0835ef5 100755
--- a/common/test_repo_setup.sh
+++ b/common/test_repo_setup.sh
@@ -40,10 +40,24 @@ create_prjgit_sample() {
 	git submodule -q add ../pkgB2 pkgB2
 	git commit -q -m "pkgB2 added"
 
-	git checkout main
+	git checkout -b base_rm_c main
 	git clean -ffxd
-	git submodule -q add -f ../pkgB1 pkgB1
-	git commit -q -m "main adding pkgB1"
+	git rm pkgC
+	git commit -q -m 'pkgC removed'
+
+	git checkout -b base_modify_c main
+	git submodule update --init pkgC
+	pushd pkgC
+	echo "mofieid" >> README.md
+	git commit -q -m "modified" README.md
+	popd
+	git commit pkgC -m "modifiedC"
+	git submodule deinit -f pkgC
+
+#	git checkout main
+#	git clean -ffxd
+#	git submodule -q add -f ../pkgB1 pkgB1
+#	git commit -q -m "main adding pkgB1"
 
 	popd
 }
-- 
2.51.1


From d5d69109061c4afec174bf7defb8ab072a861b6bd03b1d7c5b20c59f13c2ab6b Mon Sep 17 00:00:00 2001
From: Adam Majer <amajer@suse.com>
Date: Wed, 29 Oct 2025 13:01:25 +0100
Subject: [PATCH 2/3] Add command line utility to automerge conflicts

It assumes CWD is the root of the git project
---
 .gitignore                           |   2 +
 autogits.spec                        |   6 +
 common/git_utils.go                  | 212 ++++++++++++++-------------
 common/git_utils_test.go             |   2 +-
 common/pr.go                         |   2 +-
 utils/gitmodules-automerge/README.md |   9 ++
 utils/gitmodules-automerge/main.go   |  42 ++++++
 7 files changed, 173 insertions(+), 102 deletions(-)
 create mode 100644 utils/gitmodules-automerge/README.md
 create mode 100644 utils/gitmodules-automerge/main.go

diff --git a/.gitignore b/.gitignore
index 86763d8..805b4be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
 *.osc
 *.conf
+utils/gitmodules-automerge/gitmodules-automerge
+utils/hujson/hujson
diff --git a/autogits.spec b/autogits.spec
index 56264f4..a1a1c64 100644
--- a/autogits.spec
+++ b/autogits.spec
@@ -96,6 +96,7 @@ Provides:       /usr/bin/hujson
 
 %description utils
 HuJSON to JSON parser, using stdin -> stdout pipe
+gitmodules-automerge fixes conflicts in .gitmodules conflicts during merge
 
 
 %package workflow-direct
@@ -127,6 +128,9 @@ go build \
 go build \
    -C utils/hujson \
    -buildmode=pie
+go build \
+   -C utils/gitmodules-automerge \
+   -buildmode=pie
 go build \
    -C gitea-events-rabbitmq-publisher \
    -buildmode=pie
@@ -175,6 +179,7 @@ install -D -m0644 systemd/obs-status-service.service
 install -D -m0755 workflow-direct/workflow-direct                                  %{buildroot}%{_bindir}/workflow-direct
 install -D -m0755 workflow-pr/workflow-pr                                          %{buildroot}%{_bindir}/workflow-pr
 install -D -m0755 utils/hujson/hujson                                              %{buildroot}%{_bindir}/hujson
+install -D -m0755 utils/hujson/gitmodules-automerge                                %{buildroot}%{_bindir}/gitmodules-automerge
 
 %pre gitea-events-rabbitmq-publisher
 %service_add_pre gitea-events-rabbitmq-publisher.service
@@ -256,6 +261,7 @@ install -D -m0755 utils/hujson/hujson
 %files utils
 %license COPYING
 %{_bindir}/hujson
+%{_bindir}/gitmodules-automerge
 
 %files workflow-direct
 %license COPYING
diff --git a/common/git_utils.go b/common/git_utils.go
index 47c64c3..47fd52e 100644
--- a/common/git_utils.go
+++ b/common/git_utils.go
@@ -43,7 +43,8 @@ type GitDirectoryLister interface {
 }
 
 type GitSubmoduleFileConflictResolver interface {
-	GitResolveSubmoduleFileConflict(cwd, MergeBase, Head, MergeHead string) error
+	GitResolveConflicts(cwd, MergeBase, Head, MergeHead string) error
+	GitResolveSubmoduleFileConflict(s GitStatusData, cwd, mergeBase, head, mergeHead string) error
 }
 
 type GitStatusLister interface {
@@ -356,13 +357,20 @@ func (e *GitHandlerImpl) GitExecWithOutput(cwd string, params ...string) (string
 	cmd.Env = []string{
 		"GIT_CEILING_DIRECTORIES=" + e.GitPath,
 		"GIT_CONFIG_GLOBAL=/dev/null",
-		"GIT_AUTHOR_NAME=" + e.GitCommiter,
-		"GIT_COMMITTER_NAME=" + e.GitCommiter,
-		"EMAIL=not@exist@src.opensuse.org",
 		"GIT_LFS_SKIP_SMUDGE=1",
 		"GIT_LFS_SKIP_PUSH=1",
 		"GIT_SSH_COMMAND=/usr/bin/ssh -o StrictHostKeyChecking=yes",
 	}
+	if len(e.GitEmail) > 0 {
+		cmd.Env = append(cmd.Env, "EMAIL="+e.GitEmail)
+	}
+	if len(e.GitCommiter) > 0 {
+		cmd.Env = append(cmd.Env,
+			"GIT_AUTHOR_NAME="+e.GitCommiter,
+			"GIT_COMMITTER_NAME="+e.GitCommiter,
+		)
+	}
+
 	if len(ExtraGitParams) > 0 {
 		cmd.Env = append(cmd.Env, ExtraGitParams...)
 	}
@@ -1061,7 +1069,7 @@ func (e *GitHandlerImpl) GitDiffIndex(cwd, commit string) ([]GitDiffRawData, err
 	return data.([]GitDiffRawData), err
 }
 
-func (git *GitHandlerImpl) GitResolveSubmoduleFileConflict(cwd, mergeBase, head, mergeHead string) error {
+func (git *GitHandlerImpl) GitResolveConflicts(cwd, mergeBase, head, mergeHead string) error {
 	status, err := git.GitStatus(cwd)
 	if err != nil {
 		return fmt.Errorf("Status failed: %w", err)
@@ -1069,104 +1077,108 @@ func (git *GitHandlerImpl) GitResolveSubmoduleFileConflict(cwd, mergeBase, head,
 
 	// we can only resolve conflicts with .gitmodules
 	for _, s := range status {
-		if s.Status == GitStatus_Unmerged {
-			if s.Path != ".gitmodules" {
-				return fmt.Errorf("Conflict elsewhere than submodules: %s", s.Path)
+		if s.Status == GitStatus_Unmerged && s.Path == ".gitmodules" {
+			if err := git.GitResolveSubmoduleFileConflict(s, cwd, mergeBase, head, mergeHead); err != nil {
+				return err
 			}
-
-			submodules1, err := git.GitSubmoduleList(cwd, mergeBase)
-			if err != nil {
-				return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
-			}
-/*
-			submodules2, err := git.GitSubmoduleList(cwd, head)
-			if err != nil {
-				return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
-			}
-*/
-			submodules3, err := git.GitSubmoduleList(cwd, mergeHead)
-			if err != nil {
-				return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
-			}
-
-			// find modified submodules in the mergeHead
-			modifiedSubmodules := make([]string, 0, 10)
-			removedSubmodules := make([]string, 0, 10)
-			addedSubmodules := make([]string, 0, 10)
-
-			for submodulePath, oldHash := range submodules1 {
-				if newHash, found := submodules3[submodulePath]; found && newHash != oldHash {
-					modifiedSubmodules = append(modifiedSubmodules, submodulePath)
-				} else if !found {
-					removedSubmodules = append(removedSubmodules, submodulePath)
-				}
-			}
-			for submodulePath, _ := range submodules3 {
-				if _, found := submodules1[submodulePath]; !found {
-					addedSubmodules = append(addedSubmodules, submodulePath)
-				}
-			}
-
-			// We need to adjust the `submodules` list by the pending changes to the index
-			s1, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[0])
-			if err != nil {
-				return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
-			}
-			s2, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[1])
-			if err != nil {
-				return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
-			}
-			s3, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[2])
-			if err != nil {
-				return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
-			}
-
-			_, err = ParseSubmodulesFile(strings.NewReader(s1))
-			if err != nil {
-				return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
-			}
-			subs2, err := ParseSubmodulesFile(strings.NewReader(s2))
-			if err != nil {
-				return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
-			}
-			subs3, err := ParseSubmodulesFile(strings.NewReader(s3))
-			if err != nil {
-				return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
-			}
-
-			overrideSet := make([]Submodule, 0, len(addedSubmodules)+len(modifiedSubmodules))
-			for i := range subs3 {
-				if slices.Contains(addedSubmodules, subs3[i].Path) || slices.Contains(modifiedSubmodules, subs3[i].Path) {
-					overrideSet = append(overrideSet, subs3[i])
-				}
-			}
-			// merge from subs1 (merge-base), subs2 (changes in base since merge-base HEAD), subs3 (merge_source MERGE_HEAD)
-			// this will update submodules
-			SubmoduleCompare := func(a, b Submodule) int { return strings.Compare(a.Path, b.Path) }
-			CompactCompare := func(a, b Submodule) bool { return a.Path == b.Path }
-
-			// remove submodules that are removed in the PR
-			subs2 = slices.DeleteFunc(subs2, func(a Submodule) bool { return slices.Contains(removedSubmodules, a.Path) })
-
-			mergedSubs := slices.Concat(overrideSet, subs2)
-			slices.SortStableFunc(mergedSubs, SubmoduleCompare)
-			filteredSubs := slices.CompactFunc(mergedSubs, CompactCompare)
-
-			out, err := os.Create(path.Join(git.GetPath(), cwd, ".gitmodules"))
-			if err != nil {
-				return fmt.Errorf("Can't open .gitmodules for writing: %w", err)
-			}
-			if err = WriteSubmodules(filteredSubs, out); err != nil {
-				return fmt.Errorf("Can't write .gitmodules: %w", err)
-			}
-			if out.Close(); err != nil {
-				return fmt.Errorf("Can't close .gitmodules: %w", err)
-			}
-
-			git.GitExecOrPanic(cwd, "add", ".gitmodules")
-			git.GitExecOrPanic(cwd, "-c", "core.editor=true", "merge", "--continue")
+		} else if s.Status == GitStatus_Unmerged {
+			return fmt.Errorf("Cannot automatically resolve conflict: %s", s.Path)
 		}
 	}
 
+	return git.GitExec(cwd, "-c", "core.editor=true", "merge", "--continue")
+}
+
+func (git *GitHandlerImpl) GitResolveSubmoduleFileConflict(s GitStatusData, cwd, mergeBase, head, mergeHead string) error {
+	submodules1, err := git.GitSubmoduleList(cwd, mergeBase)
+	if err != nil {
+		return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
+	}
+	/*
+		submodules2, err := git.GitSubmoduleList(cwd, head)
+		if err != nil {
+			return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
+		}
+	*/
+	submodules3, err := git.GitSubmoduleList(cwd, mergeHead)
+	if err != nil {
+		return fmt.Errorf("Failed to fetch submodules during merge resolution: %w", err)
+	}
+
+	// find modified submodules in the mergeHead
+	modifiedSubmodules := make([]string, 0, 10)
+	removedSubmodules := make([]string, 0, 10)
+	addedSubmodules := make([]string, 0, 10)
+
+	for submodulePath, oldHash := range submodules1 {
+		if newHash, found := submodules3[submodulePath]; found && newHash != oldHash {
+			modifiedSubmodules = append(modifiedSubmodules, submodulePath)
+		} else if !found {
+			removedSubmodules = append(removedSubmodules, submodulePath)
+		}
+	}
+	for submodulePath, _ := range submodules3 {
+		if _, found := submodules1[submodulePath]; !found {
+			addedSubmodules = append(addedSubmodules, submodulePath)
+		}
+	}
+
+	// We need to adjust the `submodules` list by the pending changes to the index
+	s1, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[0])
+	if err != nil {
+		return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
+	}
+	s2, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[1])
+	if err != nil {
+		return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
+	}
+	s3, err := git.GitExecWithOutput(cwd, "cat-file", "blob", s.States[2])
+	if err != nil {
+		return fmt.Errorf("Failed fetching data during .gitmodules merge resoulution: %w", err)
+	}
+
+	_, err = ParseSubmodulesFile(strings.NewReader(s1))
+	if err != nil {
+		return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
+	}
+	subs2, err := ParseSubmodulesFile(strings.NewReader(s2))
+	if err != nil {
+		return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
+	}
+	subs3, err := ParseSubmodulesFile(strings.NewReader(s3))
+	if err != nil {
+		return fmt.Errorf("Failed parsing submodule file [%s] in merge: %w", s.States[0], err)
+	}
+
+	overrideSet := make([]Submodule, 0, len(addedSubmodules)+len(modifiedSubmodules))
+	for i := range subs3 {
+		if slices.Contains(addedSubmodules, subs3[i].Path) || slices.Contains(modifiedSubmodules, subs3[i].Path) {
+			overrideSet = append(overrideSet, subs3[i])
+		}
+	}
+	// merge from subs1 (merge-base), subs2 (changes in base since merge-base HEAD), subs3 (merge_source MERGE_HEAD)
+	// this will update submodules
+	SubmoduleCompare := func(a, b Submodule) int { return strings.Compare(a.Path, b.Path) }
+	CompactCompare := func(a, b Submodule) bool { return a.Path == b.Path }
+
+	// remove submodules that are removed in the PR
+	subs2 = slices.DeleteFunc(subs2, func(a Submodule) bool { return slices.Contains(removedSubmodules, a.Path) })
+
+	mergedSubs := slices.Concat(overrideSet, subs2)
+	slices.SortStableFunc(mergedSubs, SubmoduleCompare)
+	filteredSubs := slices.CompactFunc(mergedSubs, CompactCompare)
+
+	out, err := os.Create(path.Join(git.GetPath(), cwd, ".gitmodules"))
+	if err != nil {
+		return fmt.Errorf("Can't open .gitmodules for writing: %w", err)
+	}
+	if err = WriteSubmodules(filteredSubs, out); err != nil {
+		return fmt.Errorf("Can't write .gitmodules: %w", err)
+	}
+	if out.Close(); err != nil {
+		return fmt.Errorf("Can't close .gitmodules: %w", err)
+	}
+
+	git.GitExecOrPanic(cwd, "add", ".gitmodules")
 	return nil
 }
diff --git a/common/git_utils_test.go b/common/git_utils_test.go
index d3befdf..b13a540 100644
--- a/common/git_utils_test.go
+++ b/common/git_utils_test.go
@@ -207,7 +207,7 @@ func TestSubmoduleConflictResolution(t *testing.T) {
 			if err == nil {
 				t.Fatal("expected a conflict")
 			}
-			err = git.GitResolveSubmoduleFileConflict("", "main", test.checkout, test.merge)
+			err = git.GitResolveConflicts("", "main", test.checkout, test.merge)
 			if err != nil {
 				if test.merge_fail {
 					return // success
diff --git a/common/pr.go b/common/pr.go
index e5a7aa3..3391a2e 100644
--- a/common/pr.go
+++ b/common/pr.go
@@ -431,7 +431,7 @@ func (rs *PRSet) Merge(gitea GiteaReviewUnrequester, git Git) error {
 
 	err = git.GitExec(DefaultGitPrj, "merge", "--no-ff", "-m", msg, prjgit.Head.Sha)
 	if err != nil {
-		if resolveError := git.GitResolveSubmoduleFileConflict(DefaultGitPrj, prjgit.MergeBase, prjgit.Base.Sha, prjgit.Head.Sha); resolveError != nil {
+		if resolveError := git.GitResolveConflicts(DefaultGitPrj, prjgit.MergeBase, prjgit.Base.Sha, prjgit.Head.Sha); resolveError != nil {
 			return fmt.Errorf("Merge failed. (%w): %w", err, resolveError)
 		}
 	}
diff --git a/utils/gitmodules-automerge/README.md b/utils/gitmodules-automerge/README.md
new file mode 100644
index 0000000..c31057f
--- /dev/null
+++ b/utils/gitmodules-automerge/README.md
@@ -0,0 +1,9 @@
+Purpose
+-------
+
+Automatically resolve git configlicts in .gitmodules if there's a conflict
+due to a merge.
+
+It uses HEAD and MERGE_HEAD to calculate merge base and pass it to the
+conflict resolution
+
diff --git a/utils/gitmodules-automerge/main.go b/utils/gitmodules-automerge/main.go
new file mode 100644
index 0000000..c202efd
--- /dev/null
+++ b/utils/gitmodules-automerge/main.go
@@ -0,0 +1,42 @@
+package main
+
+import (
+	"os"
+	"strings"
+
+	"src.opensuse.org/autogits/common"
+)
+
+func main() {
+	cwd, err := os.Getwd()
+	if err != nil {
+		common.LogError(err)
+		return
+	}
+	gh, err := common.AllocateGitWorkTree(cwd, "", "")
+	if err != nil {
+		common.LogError(err)
+		return
+	}
+
+	git, err := gh.ReadExistingPath("")
+	if err != nil {
+		common.LogError(err)
+		return
+	}
+
+	MergeBase := strings.TrimSpace(git.GitExecWithOutputOrPanic("", "merge-base", "HEAD", "MERGE_HEAD"))
+	status, err := git.GitStatus("")
+	if err != nil {
+		common.LogError(err)
+		return
+	}
+
+	for _, s := range status {
+		if s.Path == ".gitmodules" && s.Status == common.GitStatus_Unmerged {
+			if err := git.GitResolveSubmoduleFileConflict(s, "", MergeBase, "HEAD", "MERGE_HEAD"); err != nil {
+				common.LogError(err)
+			}
+		}
+	}
+}
-- 
2.51.1


From 66a2c0565efa981542805c80d14393155b94242107b685bbb77cddfaedc9b7c0 Mon Sep 17 00:00:00 2001
From: Adam Majer <amajer@suse.com>
Date: Wed, 29 Oct 2025 13:26:16 +0100
Subject: [PATCH 3/3] utils: specfile fix

---
 autogits.spec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/autogits.spec b/autogits.spec
index a1a1c64..2a80251 100644
--- a/autogits.spec
+++ b/autogits.spec
@@ -179,7 +179,7 @@ install -D -m0644 systemd/obs-status-service.service
 install -D -m0755 workflow-direct/workflow-direct                                  %{buildroot}%{_bindir}/workflow-direct
 install -D -m0755 workflow-pr/workflow-pr                                          %{buildroot}%{_bindir}/workflow-pr
 install -D -m0755 utils/hujson/hujson                                              %{buildroot}%{_bindir}/hujson
-install -D -m0755 utils/hujson/gitmodules-automerge                                %{buildroot}%{_bindir}/gitmodules-automerge
+install -D -m0755 utils/gitmodules-automerge/gitmodules-automerge                  %{buildroot}%{_bindir}/gitmodules-automerge
 
 %pre gitea-events-rabbitmq-publisher
 %service_add_pre gitea-events-rabbitmq-publisher.service
-- 
2.51.1