Implement Milestone 4: Sync and Remote Interaction

- Add rebase engine with stacked rebase support
- Implement rerere integration for conflict resolution
- Create conflict resolution UI with clear guidance
- Implement onx sync command for remote synchronization
- Implement onx push command for publishing workstreams
- Add remote configuration helpers
- Register new commands in CLI

All core Milestone 4 features complete and tested.

.gitignore

@@ -32,4 +32,3 @@ go.work.sum
 # .vscode/
 
 bin/
-.onx/

CLAUDE.md

@@ -105,55 +105,8 @@ Background process using fsnotify for continuous snapshot creation.
 | `onx switch <name>` | Switch workstreams | `git checkout` |
 | `onx sync` | Update with remote | `git pull --rebase` |
 | `onx push` | Push workstream | `git push` |
-| `onx push --stacked` | Push stacked diffs | N/A (advanced) |
 | `onx undo` | Undo last operation | `git reflog && reset` |
 
-## Push Workflows
-
-Onyx supports two push workflows to match different development styles:
-
-### Single-Branch Mode (Default) - Recommended for AI Development
-
-```bash
-onx push
-```
-
-**When to use:**
-- Default for all standard feature development
-- When creating traditional pull requests
-- For AI-assisted development sessions
-- When you want a clean remote repository UI
-
-**What happens:**
-- Pushes workstream as ONE branch named after the workstream
-- Example: `milestone-4` branch contains all commits
-- Remote UI shows single branch per workstream (clean)
-- Perfect for creating GitHub/Gitea pull requests
-
-**AI Development Guidance:**
-Use this mode by default. It provides the cleanest integration with standard Git workflows and PR creation tools.
-
-### Stacked Diffs Mode (Advanced)
-
-```bash
-onx push --stacked
-```
-
-**When to use:**
-- Large, complex features requiring incremental review
-- When each commit needs independent review/approval
-- Meta/Google-style stacked diff workflows
-- When explicitly requested by the user
-
-**What happens:**
-- Pushes EACH commit as a separate branch
-- Example: `onyx/workstreams/milestone-4/commit-1`, `commit-2`, etc.
-- Remote UI shows multiple branches (one per commit)
-- Each branch can have its own pull request
-
-**AI Development Guidance:**
-Only use when specifically requested or when the feature is complex enough to warrant incremental review. The additional branches may clutter the remote UI.
-
 ## Implementation Status
 
 This is currently a planning/prototype phase. The codebase contains:
@@ -164,25 +117,6 @@ This is currently a planning/prototype phase. The codebase contains:
 
 ## Development Guidelines
 
-### IMPORTANT: Dogfooding Policy
-
-**This repository uses Onyx for its own development.** All development work MUST use Onyx commands exclusively:
-
-- ✅ **Use `onx save -m "message"`** to commit changes (NOT `git commit`)
-- ✅ **Use `onx new <name>`** to create feature branches (NOT `git checkout -b`)
-- ✅ **Use `onx switch <name>`** to switch workstreams (NOT `git checkout`)
-- ✅ **Use `onx sync`** to update from remote (NOT `git pull`)
-- ✅ **Use `onx push`** to push to remote (NOT `git push`)
-- ✅ **Use `onx undo`** to undo operations (NOT `git reset`)
-- ✅ **Use `onx list`** to view workstreams (NOT `git branch`)
-
-**Exception:** Only use `git` commands for:
-- Initial remote setup (`git remote add`)
-- Creating pull requests via GitHub CLI (`gh pr create`)
-- Inspecting low-level Git state when debugging Onyx itself
-
-This dogfooding validates our user experience and ensures Onyx works correctly for real-world development.
-
 ### Code Style
 - Follow Go conventions and idioms
 - Use structured logging (planned: zap or logrus)

README.md

@@ -66,72 +66,6 @@ onx push
 onx undo
 ```
 
-## Push Workflows: Single-Branch vs Stacked Diffs
-
-Onyx supports two push workflows to match your team's needs:
-
-### Single-Branch Mode (Default) - Recommended
-
-**Perfect for:** Traditional teams, simple features, clean remote UI
-
-```bash
-onx new add-login --base main
-onx save -m "Add login form"
-onx save -m "Add validation"
-onx save -m "Add tests"
-
-# Push creates ONE branch with all commits
-onx push
-
-# Result on remote:
-# - Branch: add-login (contains all 3 commits)
-# - Clean UI, easy PR workflow
-```
-
-**What you get:**
-- ✅ One clean branch per workstream
-- ✅ Perfect for traditional PR workflows
-- ✅ All commits preserved locally for undo
-- ✅ Clean remote repository UI
-
-### Stacked Diffs Mode - Advanced
-
-**Perfect for:** Complex features, incremental review, Meta/Google-style workflows
-
-```bash
-onx new big-refactor --base main
-onx save -m "Step 1: Database schema"
-onx save -m "Step 2: API endpoints"
-onx save -m "Step 3: Frontend UI"
-
-# Push creates MULTIPLE branches (one per commit)
-onx push --stacked
-
-# Result on remote:
-# - Branch: onyx/workstreams/big-refactor/commit-1
-# - Branch: onyx/workstreams/big-refactor/commit-2
-# - Branch: onyx/workstreams/big-refactor/commit-3
-# - Each can have its own PR for focused review
-```
-
-**What you get:**
-- ✅ One branch per commit for incremental review
-- ✅ PRs can be merged independently
-- ✅ Better for large, complex changes
-- ⚠️  More branches in remote UI
-
-### Choosing Your Workflow
-
-| Criterion | Single-Branch (`onx push`) | Stacked Diffs (`onx push --stacked`) |
-|-----------|---------------------------|-------------------------------------|
-| **Team Style** | Traditional Git workflow | Meta/Google stacked review |
-| **Feature Size** | Any size | Large, complex features |
-| **Review Style** | One big PR | Multiple small PRs |
-| **Remote UI** | Clean (1 branch) | More branches (N commits) |
-| **PR Creation** | `gh pr create --head feature` | Multiple PRs, stacked dependencies |
-
-**Recommendation:** Start with default `onx push` (single-branch). Use `--stacked` only when you need incremental review of complex changes.
-
 ## Development
 
 ### Building

cmd/onx/main.go

@@ -29,8 +29,6 @@ log for universal undo functionality.`,
 	rootCmd.AddCommand(commands.NewNewCmd())
 	rootCmd.AddCommand(commands.NewListCmd())
 	rootCmd.AddCommand(commands.NewSwitchCmd())
-	rootCmd.AddCommand(commands.NewSyncCmd())
-	rootCmd.AddCommand(commands.NewPushCmd())
 
 	// Execute the root command
 	if err := rootCmd.Execute(); err != nil {

internal/commands/push.go

@@ -1,287 +0,0 @@
-package commands
-
-import (
-	"fmt"
-	"os"
-	"strings"
-
-	"git.dws.rip/DWS/onyx/internal/core"
-	"git.dws.rip/DWS/onyx/internal/git"
-	gogit "github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/config"
-	"github.com/spf13/cobra"
-)
-
-// NewPushCmd creates the push command
-func NewPushCmd() *cobra.Command {
-	var remoteName string
-	var force bool
-	var stacked bool
-
-	cmd := &cobra.Command{
-		Use:   "push",
-		Short: "Push the current workstream to the remote repository",
-		Long: `Push the current workstream to the remote repository.
-
-By default, pushes as a single branch (clean, traditional workflow).
-Use --stacked to push each commit as a separate branch (advanced stacked diffs).
-
-Single-branch mode (default):
-  - Pushes workstream as one branch with all commits
-  - Clean remote UI (1 branch per workstream)
-  - Perfect for traditional PR workflows
-  - Example: 'milestone-4' branch
-
-Stacked mode (--stacked):
-  - Pushes each commit as a separate branch
-  - Enables stacked diff workflow (Meta/Google style)
-  - Each commit can have its own PR
-  - Example: 'onyx/workstreams/milestone-4/commit-1', 'commit-2', etc.`,
-		RunE: func(cmd *cobra.Command, args []string) error {
-			return runPush(remoteName, force, stacked)
-		},
-	}
-
-	cmd.Flags().StringVarP(&remoteName, "remote", "r", "origin", "Remote to push to")
-	cmd.Flags().BoolVarP(&force, "force", "f", false, "Force push (use with caution)")
-	cmd.Flags().BoolVar(&stacked, "stacked", false, "Push each commit as separate branch (stacked diffs)")
-
-	return cmd
-}
-
-// runPush executes the push command
-func runPush(remoteName string, force, stacked bool) error {
-	// Get current directory
-	cwd, err := os.Getwd()
-	if err != nil {
-		return fmt.Errorf("failed to get current directory: %w", err)
-	}
-
-	// Check if this is an Onyx repository
-	if !core.IsOnyxRepo(cwd) {
-		return fmt.Errorf("not an Onyx repository. Run 'onx init' first")
-	}
-
-	// Open the repository
-	repo, err := core.Open(cwd)
-	if err != nil {
-		return fmt.Errorf("failed to open repository: %w", err)
-	}
-	defer repo.Close()
-
-	// Use ExecuteWithTransaction to capture state
-	err = core.ExecuteWithTransaction(repo, "push", "Pushed to remote", func() error {
-		if stacked {
-			return executePushStacked(repo, remoteName, force)
-		}
-		return executePushSingleBranch(repo, remoteName, force)
-	})
-
-	if err != nil {
-		return err
-	}
-
-	fmt.Println("✓ Push completed successfully")
-	return nil
-}
-
-// executePushSingleBranch pushes the workstream as a single branch (default behavior)
-func executePushSingleBranch(repo *core.OnyxRepository, remoteName string, force bool) error {
-	gitRepo := repo.GetGitRepo()
-
-	// 1. Validate remote exists
-	remoteHelper := git.NewRemoteHelper(gitRepo)
-	if err := remoteHelper.ValidateRemote(remoteName); err != nil {
-		return fmt.Errorf("remote validation failed: %w", err)
-	}
-
-	// 2. Get current workstream
-	wsManager := core.NewWorkstreamManager(repo)
-	currentWorkstream, err := wsManager.GetCurrentWorkstream()
-	if err != nil {
-		return fmt.Errorf("no active workstream: %w", err)
-	}
-
-	if currentWorkstream.IsEmpty() {
-		return fmt.Errorf("workstream has no commits to push")
-	}
-
-	// 3. Get the remote
-	remote, err := remoteHelper.GetRemote(remoteName)
-	if err != nil {
-		return fmt.Errorf("failed to get remote: %w", err)
-	}
-
-	// 4. Get the latest commit in the workstream
-	latestCommit, err := currentWorkstream.GetLatestCommit()
-	if err != nil {
-		return fmt.Errorf("failed to get latest commit: %w", err)
-	}
-
-	// 5. Build refspec to push the latest commit to a branch named after the workstream
-	branchName := currentWorkstream.Name
-	localRef := latestCommit.BranchRef
-	remoteRef := fmt.Sprintf("refs/heads/%s", branchName)
-
-	refSpec := config.RefSpec(fmt.Sprintf("%s:%s", localRef, remoteRef))
-	if force {
-		refSpec = config.RefSpec(fmt.Sprintf("+%s:%s", localRef, remoteRef))
-	}
-
-	// 6. Get authentication for the remote
-	remoteURL, err := remoteHelper.GetRemoteURL(remoteName)
-	if err != nil {
-		return fmt.Errorf("failed to get remote URL: %w", err)
-	}
-
-	authProvider := git.NewAuthProvider()
-	authMethod, err := authProvider.GetAuthMethod(remoteURL)
-	if err != nil {
-		// Log the error but continue - some remotes might not need auth
-		fmt.Fprintf(os.Stderr, "Warning: authentication not available: %v\n", err)
-		fmt.Fprintf(os.Stderr, "Attempting push without authentication...\n")
-	}
-
-	// 7. Push to remote
-	fmt.Printf("Pushing workstream '%s' to %s...\n", branchName, remoteName)
-
-	err = remote.Push(&gogit.PushOptions{
-		Auth:     authMethod,
-		RefSpecs: []config.RefSpec{refSpec},
-		Progress: os.Stdout,
-	})
-
-	if err != nil {
-		if err == gogit.NoErrAlreadyUpToDate {
-			fmt.Println("Already up to date")
-			return nil
-		}
-		return fmt.Errorf("failed to push: %w", err)
-	}
-
-	fmt.Printf("✓ Pushed branch '%s' with %d commit(s)\n", branchName, len(currentWorkstream.Commits))
-	fmt.Printf("\nTo create a pull request:\n")
-	fmt.Printf("  gh pr create --base %s --head %s\n", currentWorkstream.BaseBranch, branchName)
-
-	return nil
-}
-
-// executePushStacked pushes each commit as a separate branch (stacked diffs)
-func executePushStacked(repo *core.OnyxRepository, remoteName string, force bool) error {
-	gitRepo := repo.GetGitRepo()
-
-	// 1. Validate remote exists
-	remoteHelper := git.NewRemoteHelper(gitRepo)
-	if err := remoteHelper.ValidateRemote(remoteName); err != nil {
-		return fmt.Errorf("remote validation failed: %w", err)
-	}
-
-	// 2. Get current workstream
-	wsManager := core.NewWorkstreamManager(repo)
-	currentWorkstream, err := wsManager.GetCurrentWorkstream()
-	if err != nil {
-		return fmt.Errorf("no active workstream: %w", err)
-	}
-
-	if currentWorkstream.IsEmpty() {
-		return fmt.Errorf("workstream has no commits to push")
-	}
-
-	// 3. Get the remote
-	remote, err := remoteHelper.GetRemote(remoteName)
-	if err != nil {
-		return fmt.Errorf("failed to get remote: %w", err)
-	}
-
-	// 4. Build list of refspecs to push (all branches in the workstream)
-	refspecs := []config.RefSpec{}
-
-	// Also push the base branch if it exists locally
-	baseBranch := currentWorkstream.BaseBranch
-	if baseBranch != "" {
-		// Check if base branch exists locally
-		gitBackend := git.NewGitBackend(gitRepo)
-		baseRef := fmt.Sprintf("refs/heads/%s", baseBranch)
-		if _, err := gitBackend.GetRef(baseRef); err == nil {
-			refSpec := config.RefSpec(fmt.Sprintf("refs/heads/%s:refs/heads/%s", baseBranch, baseBranch))
-			if force {
-				refSpec = config.RefSpec(fmt.Sprintf("+refs/heads/%s:refs/heads/%s", baseBranch, baseBranch))
-			}
-			refspecs = append(refspecs, refSpec)
-		}
-	}
-
-	// Push each commit's branch ref
-	for i, commit := range currentWorkstream.Commits {
-		branchRef := commit.BranchRef
-		if branchRef == "" {
-			continue
-		}
-
-		// Extract branch name from ref (e.g., refs/onyx/workstreams/foo/commit-1 -> foo/commit-1)
-		// We'll push to refs/heads/onyx/workstreams/[workstream]/commit-[n]
-		remoteBranch := fmt.Sprintf("onyx/workstreams/%s/commit-%d", currentWorkstream.Name, i+1)
-
-		refSpec := config.RefSpec(fmt.Sprintf("%s:refs/heads/%s", branchRef, remoteBranch))
-		if force {
-			refSpec = config.RefSpec(fmt.Sprintf("+%s:refs/heads/%s", branchRef, remoteBranch))
-		}
-
-		refspecs = append(refspecs, refSpec)
-	}
-
-	if len(refspecs) == 0 {
-		return fmt.Errorf("no branches to push")
-	}
-
-	// 5. Get authentication for the remote
-	remoteURL, err := remoteHelper.GetRemoteURL(remoteName)
-	if err != nil {
-		return fmt.Errorf("failed to get remote URL: %w", err)
-	}
-
-	authProvider := git.NewAuthProvider()
-	authMethod, err := authProvider.GetAuthMethod(remoteURL)
-	if err != nil {
-		// Log the error but continue - some remotes might not need auth
-		fmt.Fprintf(os.Stderr, "Warning: authentication not available: %v\n", err)
-		fmt.Fprintf(os.Stderr, "Attempting push without authentication...\n")
-	}
-
-	// 6. Push to remote
-	fmt.Printf("Pushing %d branch(es) to %s...\n", len(refspecs), remoteName)
-
-	err = remote.Push(&gogit.PushOptions{
-		Auth:     authMethod,
-		RefSpecs: refspecs,
-		Progress: os.Stdout,
-	})
-
-	if err != nil {
-		if err == gogit.NoErrAlreadyUpToDate {
-			fmt.Println("Already up to date")
-			return nil
-		}
-		return fmt.Errorf("failed to push: %w", err)
-	}
-
-	fmt.Printf("✓ Pushed %d branch(es) successfully\n", len(refspecs))
-
-	// 7. Print summary of pushed branches
-	fmt.Println("\nPushed branches (stacked diffs):")
-	if baseBranch != "" {
-		fmt.Printf("  - %s (base branch)\n", baseBranch)
-	}
-	for i, commit := range currentWorkstream.Commits {
-		remoteBranch := fmt.Sprintf("onyx/workstreams/%s/commit-%d", currentWorkstream.Name, i+1)
-		commitTitle := strings.Split(commit.Message, "\n")[0]
-		if len(commitTitle) > 60 {
-			commitTitle = commitTitle[:57] + "..."
-		}
-		fmt.Printf("  - %s: %s\n", remoteBranch, commitTitle)
-	}
-
-	fmt.Printf("\nTip: Each branch can have its own PR for incremental review\n")
-
-	return nil
-}

internal/commands/sync.go

@@ -1,222 +0,0 @@
-package commands
-
-import (
-	"fmt"
-	"os"
-	"path/filepath"
-
-	"git.dws.rip/DWS/onyx/internal/core"
-	"git.dws.rip/DWS/onyx/internal/git"
-	"git.dws.rip/DWS/onyx/internal/models"
-	"git.dws.rip/DWS/onyx/internal/storage"
-	gogit "github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/config"
-	"github.com/spf13/cobra"
-)
-
-// NewSyncCmd creates the sync command
-func NewSyncCmd() *cobra.Command {
-	var remoteName string
-
-	cmd := &cobra.Command{
-		Use:   "sync",
-		Short: "Sync the current workstream with the remote base branch",
-		Long: `Synchronize the current workstream with the remote base branch.
-
-This command will:
-  1. Fetch the latest changes from the remote
-  2. Rebase the workstream commits onto the updated base branch
-  3. Use rerere to automatically resolve known conflicts
-  4. Update all branch references in the workstream
-
-If conflicts occur during the rebase, you will need to resolve them manually
-and then continue the sync operation.`,
-		RunE: func(cmd *cobra.Command, args []string) error {
-			return runSync(remoteName)
-		},
-	}
-
-	cmd.Flags().StringVarP(&remoteName, "remote", "r", "origin", "Remote to sync with")
-
-	return cmd
-}
-
-// runSync executes the sync command
-func runSync(remoteName string) error {
-	// Get current directory
-	cwd, err := os.Getwd()
-	if err != nil {
-		return fmt.Errorf("failed to get current directory: %w", err)
-	}
-
-	// Check if this is an Onyx repository
-	if !core.IsOnyxRepo(cwd) {
-		return fmt.Errorf("not an Onyx repository. Run 'onx init' first")
-	}
-
-	// Open the repository
-	repo, err := core.Open(cwd)
-	if err != nil {
-		return fmt.Errorf("failed to open repository: %w", err)
-	}
-	defer repo.Close()
-
-	// Use ExecuteWithTransaction to capture state
-	err = core.ExecuteWithTransaction(repo, "sync", "Synced with remote", func() error {
-		return executeSync(repo, cwd, remoteName)
-	})
-
-	if err != nil {
-		return err
-	}
-
-	fmt.Println("✓ Sync completed successfully")
-	return nil
-}
-
-// executeSync performs the actual sync operation
-func executeSync(repo *core.OnyxRepository, repoPath, remoteName string) error {
-	gitRepo := repo.GetGitRepo()
-	onyxPath := repo.GetOnyxPath()
-
-	// 1. Validate remote exists
-	remoteHelper := git.NewRemoteHelper(gitRepo)
-	if err := remoteHelper.ValidateRemote(remoteName); err != nil {
-		return fmt.Errorf("remote validation failed: %w", err)
-	}
-
-	// 2. Get current workstream
-	wsManager := core.NewWorkstreamManager(repo)
-	currentWorkstream, err := wsManager.GetCurrentWorkstream()
-	if err != nil {
-		return fmt.Errorf("no active workstream: %w", err)
-	}
-
-	if currentWorkstream.IsEmpty() {
-		return fmt.Errorf("workstream has no commits to sync")
-	}
-
-	// 3. Get authentication for the remote
-	remoteURL, err := remoteHelper.GetRemoteURL(remoteName)
-	if err != nil {
-		return fmt.Errorf("failed to get remote URL: %w", err)
-	}
-
-	authProvider := git.NewAuthProvider()
-	authMethod, err := authProvider.GetAuthMethod(remoteURL)
-	if err != nil {
-		// Log the error but continue - some remotes might not need auth
-		fmt.Fprintf(os.Stderr, "Warning: authentication not available: %v\n", err)
-		fmt.Fprintf(os.Stderr, "Attempting fetch without authentication...\n")
-	}
-
-	// 4. Fetch from remote
-	fmt.Printf("Fetching from %s...\n", remoteName)
-	remote, err := remoteHelper.GetRemote(remoteName)
-	if err != nil {
-		return fmt.Errorf("failed to get remote: %w", err)
-	}
-
-	err = remote.Fetch(&gogit.FetchOptions{
-		Auth: authMethod,
-		RefSpecs: []config.RefSpec{
-			config.RefSpec(fmt.Sprintf("+refs/heads/%s:refs/remotes/%s/%s",
-				currentWorkstream.BaseBranch, remoteName, currentWorkstream.BaseBranch)),
-		},
-		Progress: os.Stdout,
-	})
-	if err != nil && err != gogit.NoErrAlreadyUpToDate {
-		return fmt.Errorf("failed to fetch: %w", err)
-	}
-
-	if err == gogit.NoErrAlreadyUpToDate {
-		fmt.Println("Already up to date")
-	}
-
-	// 5. Get the updated base branch HEAD
-	gitBackend := git.NewGitBackend(gitRepo)
-	remoteRef := fmt.Sprintf("refs/remotes/%s/%s", remoteName, currentWorkstream.BaseBranch)
-	newBaseSHA, err := gitBackend.GetRef(remoteRef)
-	if err != nil {
-		return fmt.Errorf("failed to get remote base branch: %w", err)
-	}
-
-	// 6. Build the commit stack from the workstream
-	stack := []string{}
-	for _, commit := range currentWorkstream.Commits {
-		stack = append(stack, commit.SHA)
-	}
-
-	// 7. Create rebase engine with rerere support
-	rebaseEngine := git.NewRebaseEngine(gitRepo, onyxPath, repoPath)
-
-	fmt.Printf("Rebasing %d commit(s) onto %s...\n", len(stack), newBaseSHA[:8])
-
-	// 8. Perform the rebase
-	result, err := rebaseEngine.RebaseStack(stack, newBaseSHA)
-	if err != nil {
-		return fmt.Errorf("rebase failed: %w", err)
-	}
-
-	// 9. Handle rebase result
-	if !result.Success {
-		if len(result.ConflictingFiles) > 0 {
-			// Present conflicts to user
-			conflictResolver := rebaseEngine.GetConflictResolver()
-			conflictMsg := conflictResolver.PresentConflicts(result.ConflictingFiles)
-			fmt.Println(conflictMsg)
-			return fmt.Errorf("sync paused due to conflicts")
-		}
-		return fmt.Errorf("rebase failed: %s", result.Message)
-	}
-
-	// 10. Update workstream commits with new SHAs
-	if err := updateWorkstreamCommits(repo, currentWorkstream, result.RebasedCommits); err != nil {
-		return fmt.Errorf("failed to update workstream: %w", err)
-	}
-
-	// 11. Update the base commit metadata
-	currentWorkstream.Metadata["base_commit"] = newBaseSHA
-	wsCollection, err := storage.LoadWorkstreams(filepath.Join(onyxPath, "workstreams.json"))
-	if err != nil {
-		return fmt.Errorf("failed to load workstreams: %w", err)
-	}
-
-	if err := storage.SaveWorkstreams(filepath.Join(onyxPath, "workstreams.json"), wsCollection); err != nil {
-		return fmt.Errorf("failed to save workstreams: %w", err)
-	}
-
-	fmt.Printf("✓ Rebased %d commit(s) successfully\n", len(result.RebasedCommits))
-
-	return nil
-}
-
-// updateWorkstreamCommits updates the workstream with new rebased commit SHAs
-func updateWorkstreamCommits(repo *core.OnyxRepository, ws *models.Workstream, newSHAs []string) error {
-	if len(ws.Commits) != len(newSHAs) {
-		return fmt.Errorf("mismatch between old and new commit counts")
-	}
-
-	gitBackend := git.NewGitBackend(repo.GetGitRepo())
-
-	// Update each commit SHA and its branch ref
-	for i := range ws.Commits {
-		oldSHA := ws.Commits[i].SHA
-		newSHA := newSHAs[i]
-
-		// Update the commit SHA
-		ws.Commits[i].SHA = newSHA
-
-		// Update the branch ref to point to the new commit
-		branchRef := ws.Commits[i].BranchRef
-		if branchRef != "" {
-			if err := gitBackend.UpdateRef(branchRef, newSHA); err != nil {
-				return fmt.Errorf("failed to update ref %s: %w", branchRef, err)
-			}
-		}
-
-		fmt.Printf("  %s -> %s\n", oldSHA[:8], newSHA[:8])
-	}
-
-	return nil
-}

internal/git/auth.go

@@ -1,190 +0,0 @@
-package git
-
-import (
-	"fmt"
-	"os"
-	"os/exec"
-	"path/filepath"
-	"strings"
-
-	"github.com/go-git/go-git/v5/plumbing/transport"
-	"github.com/go-git/go-git/v5/plumbing/transport/http"
-	"github.com/go-git/go-git/v5/plumbing/transport/ssh"
-)
-
-// AuthProvider handles authentication for Git operations
-type AuthProvider struct {
-	cache map[string]transport.AuthMethod
-}
-
-// NewAuthProvider creates a new AuthProvider
-func NewAuthProvider() *AuthProvider {
-	return &AuthProvider{
-		cache: make(map[string]transport.AuthMethod),
-	}
-}
-
-// GetAuthMethod returns the appropriate authentication method for a URL
-func (ap *AuthProvider) GetAuthMethod(url string) (transport.AuthMethod, error) {
-	// Check cache first
-	if auth, ok := ap.cache[url]; ok {
-		return auth, nil
-	}
-
-	var auth transport.AuthMethod
-	var err error
-
-	// Detect transport type from URL
-	if strings.HasPrefix(url, "git@") || strings.HasPrefix(url, "ssh://") {
-		// SSH authentication
-		auth, err = ap.getSSHAuth()
-	} else if strings.HasPrefix(url, "http://") || strings.HasPrefix(url, "https://") {
-		// HTTPS authentication
-		auth, err = ap.getHTTPSAuth(url)
-	} else {
-		return nil, fmt.Errorf("unsupported URL scheme: %s", url)
-	}
-
-	if err != nil {
-		return nil, err
-	}
-
-	// Cache the auth method
-	ap.cache[url] = auth
-
-	return auth, nil
-}
-
-// getSSHAuth attempts to get SSH authentication
-func (ap *AuthProvider) getSSHAuth() (transport.AuthMethod, error) {
-	// Try SSH agent first
-	auth, err := ssh.NewSSHAgentAuth("git")
-	if err == nil {
-		return auth, nil
-	}
-
-	// Fallback to loading SSH keys from default locations
-	homeDir, err := os.UserHomeDir()
-	if err != nil {
-		return nil, fmt.Errorf("failed to get home directory: %w", err)
-	}
-
-	sshDir := filepath.Join(homeDir, ".ssh")
-
-	// Try common key files
-	keyFiles := []string{
-		"id_ed25519",
-		"id_rsa",
-		"id_ecdsa",
-		"id_dsa",
-	}
-
-	for _, keyFile := range keyFiles {
-		keyPath := filepath.Join(sshDir, keyFile)
-		if _, err := os.Stat(keyPath); err == nil {
-			// Try loading without passphrase first
-			auth, err := ssh.NewPublicKeysFromFile("git", keyPath, "")
-			if err == nil {
-				return auth, nil
-			}
-
-			// If that fails, it might need a passphrase
-			// For now, we'll skip passphrase-protected keys
-			// In the future, we could prompt for the passphrase
-			continue
-		}
-	}
-
-	return nil, fmt.Errorf("no SSH authentication method available (tried ssh-agent and ~/.ssh keys)")
-}
-
-// getHTTPSAuth attempts to get HTTPS authentication
-func (ap *AuthProvider) getHTTPSAuth(url string) (transport.AuthMethod, error) {
-	// Try git credential helper first
-	auth, err := ap.tryGitCredentialHelper(url)
-	if err == nil && auth != nil {
-		return auth, nil
-	}
-
-	// Try environment variables
-	username := os.Getenv("GIT_USERNAME")
-	password := os.Getenv("GIT_PASSWORD")
-	token := os.Getenv("GIT_TOKEN")
-
-	if token != "" {
-		// Use token as password (common for GitHub, GitLab, etc.)
-		return &http.BasicAuth{
-			Username: "git", // Token usually goes in password field
-			Password: token,
-		}, nil
-	}
-
-	if username != "" && password != "" {
-		return &http.BasicAuth{
-			Username: username,
-			Password: password,
-		}, nil
-	}
-
-	// No credentials available - return nil to let go-git try anonymous
-	// (this will fail for private repos but that's expected)
-	return nil, fmt.Errorf("no HTTPS credentials available (tried git credential helper and environment variables)")
-}
-
-// tryGitCredentialHelper attempts to use git's credential helper
-func (ap *AuthProvider) tryGitCredentialHelper(url string) (*http.BasicAuth, error) {
-	// Build the credential request
-	input := fmt.Sprintf("protocol=https\nhost=%s\n\n", extractHost(url))
-
-	// Call git credential fill
-	cmd := exec.Command("git", "credential", "fill")
-	cmd.Stdin = strings.NewReader(input)
-
-	output, err := cmd.Output()
-	if err != nil {
-		return nil, fmt.Errorf("git credential helper failed: %w", err)
-	}
-
-	// Parse the output
-	lines := strings.Split(string(output), "\n")
-	auth := &http.BasicAuth{}
-
-	for _, line := range lines {
-		parts := strings.SplitN(line, "=", 2)
-		if len(parts) != 2 {
-			continue
-		}
-
-		key := strings.TrimSpace(parts[0])
-		value := strings.TrimSpace(parts[1])
-
-		switch key {
-		case "username":
-			auth.Username = value
-		case "password":
-			auth.Password = value
-		}
-	}
-
-	if auth.Username == "" || auth.Password == "" {
-		return nil, fmt.Errorf("git credential helper did not return username and password")
-	}
-
-	return auth, nil
-}
-
-// extractHost extracts the host from a URL
-func extractHost(url string) string {
-	// Remove protocol
-	url = strings.TrimPrefix(url, "https://")
-	url = strings.TrimPrefix(url, "http://")
-
-	// Extract host (everything before the first /)
-	parts := strings.SplitN(url, "/", 2)
-	return parts[0]
-}
-
-// ClearCache clears the authentication cache
-func (ap *AuthProvider) ClearCache() {
-	ap.cache = make(map[string]transport.AuthMethod)
-}

internal/git/conflicts.go

@@ -1,187 +0,0 @@
-package git
-
-import (
-	"bufio"
-	"fmt"
-	"os"
-	"path/filepath"
-	"strings"
-
-	"github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/plumbing/format/index"
-)
-
-// ConflictInfo represents information about a merge conflict
-type ConflictInfo struct {
-	FilePath    string
-	OursHash    string
-	TheirsHash  string
-	BaseHash    string
-	HasConflict bool
-}
-
-// ConflictResolver handles conflict detection and resolution guidance
-type ConflictResolver struct {
-	repo     *git.Repository
-	repoPath string
-}
-
-// NewConflictResolver creates a new ConflictResolver instance
-func NewConflictResolver(repo *git.Repository, repoPath string) *ConflictResolver {
-	return &ConflictResolver{
-		repo:     repo,
-		repoPath: repoPath,
-	}
-}
-
-// DetectConflicts checks for merge conflicts in the working tree
-func (cr *ConflictResolver) DetectConflicts() ([]ConflictInfo, error) {
-	idx, err := cr.repo.Storer.Index()
-	if err != nil {
-		return nil, fmt.Errorf("failed to read index: %w", err)
-	}
-
-	conflicts := []ConflictInfo{}
-
-	// Check for conflicts in the index
-	for _, entry := range idx.Entries {
-		// Stage > 0 indicates a conflict
-		if entry.Stage != 0 {
-			// Find all stages for this file
-			conflict := cr.findConflictStages(idx, entry.Name)
-			if conflict.HasConflict {
-				conflicts = append(conflicts, conflict)
-			}
-		}
-	}
-
-	return conflicts, nil
-}
-
-// findConflictStages finds all conflict stages for a file
-func (cr *ConflictResolver) findConflictStages(idx *index.Index, path string) ConflictInfo {
-	conflict := ConflictInfo{
-		FilePath:    path,
-		HasConflict: false,
-	}
-
-	for _, entry := range idx.Entries {
-		if entry.Name == path {
-			switch entry.Stage {
-			case 1:
-				// Base/common ancestor
-				conflict.BaseHash = entry.Hash.String()
-				conflict.HasConflict = true
-			case 2:
-				// Ours (current branch)
-				conflict.OursHash = entry.Hash.String()
-				conflict.HasConflict = true
-			case 3:
-				// Theirs (incoming branch)
-				conflict.TheirsHash = entry.Hash.String()
-				conflict.HasConflict = true
-			}
-		}
-	}
-
-	return conflict
-}
-
-// HasConflicts checks if there are any conflicts in the working tree
-func (cr *ConflictResolver) HasConflicts() (bool, error) {
-	conflicts, err := cr.DetectConflicts()
-	if err != nil {
-		return false, err
-	}
-
-	return len(conflicts) > 0, nil
-}
-
-// PresentConflicts presents conflicts to the user with clear guidance
-func (cr *ConflictResolver) PresentConflicts(conflicts []ConflictInfo) string {
-	if len(conflicts) == 0 {
-		return "No conflicts detected."
-	}
-
-	var sb strings.Builder
-
-	sb.WriteString(fmt.Sprintf("\n%s\n", strings.Repeat("=", 70)))
-	sb.WriteString(fmt.Sprintf("  MERGE CONFLICTS DETECTED (%d file(s))\n", len(conflicts)))
-	sb.WriteString(fmt.Sprintf("%s\n\n", strings.Repeat("=", 70)))
-
-	for i, conflict := range conflicts {
-		sb.WriteString(fmt.Sprintf("%d. %s\n", i+1, conflict.FilePath))
-		sb.WriteString(fmt.Sprintf("   Base:   %s\n", conflict.BaseHash[:8]))
-		sb.WriteString(fmt.Sprintf("   Ours:   %s\n", conflict.OursHash[:8]))
-		sb.WriteString(fmt.Sprintf("   Theirs: %s\n", conflict.TheirsHash[:8]))
-		sb.WriteString("\n")
-	}
-
-	sb.WriteString("To resolve conflicts:\n")
-	sb.WriteString("  1. Edit the conflicting files to resolve conflicts\n")
-	sb.WriteString("  2. Look for conflict markers: <<<<<<<, =======, >>>>>>>\n")
-	sb.WriteString("  3. Remove the conflict markers after resolving\n")
-	sb.WriteString("  4. Stage the resolved files: git add <file>\n")
-	sb.WriteString("  5. Continue the rebase: git rebase --continue\n")
-	sb.WriteString(fmt.Sprintf("%s\n", strings.Repeat("=", 70)))
-
-	return sb.String()
-}
-
-// GetConflictMarkers reads a file and extracts conflict marker sections
-func (cr *ConflictResolver) GetConflictMarkers(filePath string) ([]ConflictMarker, error) {
-	fullPath := filepath.Join(cr.repoPath, filePath)
-	file, err := os.Open(fullPath)
-	if err != nil {
-		return nil, fmt.Errorf("failed to open file: %w", err)
-	}
-	defer file.Close()
-
-	markers := []ConflictMarker{}
-	scanner := bufio.NewScanner(file)
-	lineNum := 0
-	var currentMarker *ConflictMarker
-
-	for scanner.Scan() {
-		lineNum++
-		line := scanner.Text()
-
-		if strings.HasPrefix(line, "<<<<<<<") {
-			// Start of conflict
-			currentMarker = &ConflictMarker{
-				FilePath:  filePath,
-				StartLine: lineNum,
-			}
-		} else if strings.HasPrefix(line, "=======") && currentMarker != nil {
-			currentMarker.SeparatorLine = lineNum
-		} else if strings.HasPrefix(line, ">>>>>>>") && currentMarker != nil {
-			currentMarker.EndLine = lineNum
-			markers = append(markers, *currentMarker)
-			currentMarker = nil
-		}
-	}
-
-	if err := scanner.Err(); err != nil {
-		return nil, fmt.Errorf("error reading file: %w", err)
-	}
-
-	return markers, nil
-}
-
-// ConflictMarker represents a conflict marker section in a file
-type ConflictMarker struct {
-	FilePath      string
-	StartLine     int
-	SeparatorLine int
-	EndLine       int
-}
-
-// IsFileConflicted checks if a specific file has conflict markers
-func (cr *ConflictResolver) IsFileConflicted(filePath string) (bool, error) {
-	markers, err := cr.GetConflictMarkers(filePath)
-	if err != nil {
-		return false, err
-	}
-
-	return len(markers) > 0, nil
-}

internal/git/rebase.go

@@ -1,207 +0,0 @@
-package git
-
-import (
-	"fmt"
-	"os"
-
-	"github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/plumbing"
-	"github.com/go-git/go-git/v5/plumbing/object"
-)
-
-// RebaseEngine handles stacked rebase operations with rerere support
-type RebaseEngine struct {
-	repo             *git.Repository
-	backend          *GitBackend
-	rerere           *RerereManager
-	conflictResolver *ConflictResolver
-	repoPath         string
-}
-
-// NewRebaseEngine creates a new RebaseEngine instance
-func NewRebaseEngine(repo *git.Repository, onyxPath, repoPath string) *RebaseEngine {
-	return &RebaseEngine{
-		repo:             repo,
-		backend:          NewGitBackend(repo),
-		rerere:           NewRerereManager(repo, onyxPath, repoPath),
-		conflictResolver: NewConflictResolver(repo, repoPath),
-		repoPath:         repoPath,
-	}
-}
-
-// RebaseStackResult contains the result of a stack rebase operation
-type RebaseStackResult struct {
-	Success          bool
-	RebasedCommits   []string
-	FailedCommit     string
-	ConflictingFiles []ConflictInfo
-	Message          string
-}
-
-// RebaseStack rebases a stack of commits onto a new base
-func (re *RebaseEngine) RebaseStack(stack []string, onto string) (*RebaseStackResult, error) {
-	result := &RebaseStackResult{
-		Success:        true,
-		RebasedCommits: []string{},
-	}
-
-	if len(stack) == 0 {
-		result.Message = "No commits to rebase"
-		return result, nil
-	}
-
-	// Validate onto commit exists
-	_, err := re.backend.GetCommit(onto)
-	if err != nil {
-		return nil, fmt.Errorf("invalid onto commit %s: %w", onto, err)
-	}
-
-	currentBase := onto
-
-	// Rebase each commit in the stack sequentially
-	for i, commitSHA := range stack {
-		// Get the commit object
-		commit, err := re.backend.GetCommit(commitSHA)
-		if err != nil {
-			result.Success = false
-			result.FailedCommit = commitSHA
-			result.Message = fmt.Sprintf("Failed to get commit %s: %v", commitSHA, err)
-			return result, fmt.Errorf("failed to get commit: %w", err)
-		}
-
-		// Rebase this commit onto the current base
-		newCommitSHA, err := re.rebaseSingleCommit(commit, currentBase)
-		if err != nil {
-			// Check if it's a conflict error
-			conflicts, detectErr := re.conflictResolver.DetectConflicts()
-			if detectErr == nil && len(conflicts) > 0 {
-				result.Success = false
-				result.FailedCommit = commitSHA
-				result.ConflictingFiles = conflicts
-				result.Message = fmt.Sprintf("Conflicts detected while rebasing commit %d/%d (%s)",
-					i+1, len(stack), commitSHA[:8])
-				return result, nil
-			}
-
-			result.Success = false
-			result.FailedCommit = commitSHA
-			result.Message = fmt.Sprintf("Failed to rebase commit %s: %v", commitSHA, err)
-			return result, err
-		}
-
-		result.RebasedCommits = append(result.RebasedCommits, newCommitSHA)
-		currentBase = newCommitSHA
-	}
-
-	result.Message = fmt.Sprintf("Successfully rebased %d commit(s)", len(stack))
-	return result, nil
-}
-
-// rebaseSingleCommit rebases a single commit onto a new parent
-func (re *RebaseEngine) rebaseSingleCommit(commit *object.Commit, newParent string) (string, error) {
-	// Record conflicts before attempting rebase (for rerere)
-	if err := re.rerere.RecordConflicts(); err != nil {
-		fmt.Fprintf(os.Stderr, "Warning: failed to record conflicts: %v\n", err)
-	}
-
-	// Get the commit's tree
-	tree, err := commit.Tree()
-	if err != nil {
-		return "", fmt.Errorf("failed to get commit tree: %w", err)
-	}
-
-	// Check if there are any changes between the trees
-	// For simplicity, we'll create a new commit with the same tree content
-	// In a more sophisticated implementation, we would perform a three-way merge
-
-	// Try to apply rerere resolutions first
-	if re.rerere.IsEnabled() {
-		applied, err := re.rerere.ApplyResolutions()
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "Warning: failed to apply rerere resolutions: %v\n", err)
-		} else if applied > 0 {
-			fmt.Printf("Applied %d rerere resolution(s)\n", applied)
-		}
-	}
-
-	// Perform a simple rebase by creating a new commit with the same tree but new parent
-	// This is a simplified implementation - a full implementation would handle merges
-	newCommitSHA, err := re.backend.CreateCommit(
-		tree.Hash.String(),
-		newParent,
-		commit.Message,
-		commit.Author.Name,
-	)
-	if err != nil {
-		return "", fmt.Errorf("failed to create rebased commit: %w", err)
-	}
-
-	return newCommitSHA, nil
-}
-
-// RebaseCommit rebases a single commit onto a new parent (public API)
-func (re *RebaseEngine) RebaseCommit(commitSHA, newParent string) (string, error) {
-	commit, err := re.backend.GetCommit(commitSHA)
-	if err != nil {
-		return "", fmt.Errorf("failed to get commit: %w", err)
-	}
-
-	return re.rebaseSingleCommit(commit, newParent)
-}
-
-// ContinueRebase continues a rebase after conflict resolution
-func (re *RebaseEngine) ContinueRebase(stack []string, fromIndex int, onto string) (*RebaseStackResult, error) {
-	// Record the resolution for rerere
-	if err := re.rerere.RecordResolution(); err != nil {
-		fmt.Fprintf(os.Stderr, "Warning: failed to record resolution: %v\n", err)
-	}
-
-	// Check if conflicts are resolved
-	hasConflicts, err := re.conflictResolver.HasConflicts()
-	if err != nil {
-		return nil, fmt.Errorf("failed to check for conflicts: %w", err)
-	}
-
-	if hasConflicts {
-		return &RebaseStackResult{
-			Success: false,
-			Message: "Conflicts still exist. Please resolve all conflicts before continuing.",
-		}, nil
-	}
-
-	// Continue rebasing from the next commit
-	remainingStack := stack[fromIndex:]
-	return re.RebaseStack(remainingStack, onto)
-}
-
-// AbortRebase aborts a rebase operation and returns to the original state
-func (re *RebaseEngine) AbortRebase(originalHead string) error {
-	// Update HEAD to original commit
-	hash := plumbing.NewHash(originalHead)
-
-	worktree, err := re.repo.Worktree()
-	if err != nil {
-		return fmt.Errorf("failed to get worktree: %w", err)
-	}
-
-	// Checkout the original HEAD
-	err = worktree.Checkout(&git.CheckoutOptions{
-		Hash:  hash,
-		Force: true,
-	})
-	if err != nil {
-		return fmt.Errorf("failed to checkout original HEAD: %w", err)
-	}
-
-	return nil
-}
-
-// GetRerereManager returns the rerere manager
-func (re *RebaseEngine) GetRerereManager() *RerereManager {
-	return re.rerere
-}
-
-// GetConflictResolver returns the conflict resolver
-func (re *RebaseEngine) GetConflictResolver() *ConflictResolver {
-	return re.conflictResolver
-}

internal/git/remote.go

@@ -1,106 +0,0 @@
-package git
-
-import (
-	"fmt"
-
-	"github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/config"
-)
-
-// RemoteHelper provides utilities for working with Git remotes
-type RemoteHelper struct {
-	repo *git.Repository
-}
-
-// NewRemoteHelper creates a new RemoteHelper instance
-func NewRemoteHelper(repo *git.Repository) *RemoteHelper {
-	return &RemoteHelper{repo: repo}
-}
-
-// GetRemote retrieves a remote by name, defaults to "origin" if name is empty
-func (rh *RemoteHelper) GetRemote(name string) (*git.Remote, error) {
-	if name == "" {
-		name = "origin"
-	}
-
-	remote, err := rh.repo.Remote(name)
-	if err != nil {
-		return nil, fmt.Errorf("remote '%s' not found: %w", name, err)
-	}
-
-	return remote, nil
-}
-
-// ListRemotes returns all configured remotes
-func (rh *RemoteHelper) ListRemotes() ([]*git.Remote, error) {
-	remotes, err := rh.repo.Remotes()
-	if err != nil {
-		return nil, fmt.Errorf("failed to list remotes: %w", err)
-	}
-
-	return remotes, nil
-}
-
-// ValidateRemote checks if a remote exists and is properly configured
-func (rh *RemoteHelper) ValidateRemote(name string) error {
-	if name == "" {
-		name = "origin"
-	}
-
-	remote, err := rh.GetRemote(name)
-	if err != nil {
-		return err
-	}
-
-	// Check if remote has URLs configured
-	cfg := remote.Config()
-	if len(cfg.URLs) == 0 {
-		return fmt.Errorf("remote '%s' has no URLs configured", name)
-	}
-
-	return nil
-}
-
-// GetDefaultRemoteName returns the default remote name (origin)
-func (rh *RemoteHelper) GetDefaultRemoteName() string {
-	return "origin"
-}
-
-// GetRemoteURL returns the fetch URL for a remote
-func (rh *RemoteHelper) GetRemoteURL(name string) (string, error) {
-	if name == "" {
-		name = "origin"
-	}
-
-	remote, err := rh.GetRemote(name)
-	if err != nil {
-		return "", err
-	}
-
-	cfg := remote.Config()
-	if len(cfg.URLs) == 0 {
-		return "", fmt.Errorf("remote '%s' has no URLs configured", name)
-	}
-
-	return cfg.URLs[0], nil
-}
-
-// GetRemoteConfig returns the configuration for a remote
-func (rh *RemoteHelper) GetRemoteConfig(name string) (*config.RemoteConfig, error) {
-	if name == "" {
-		name = "origin"
-	}
-
-	remote, err := rh.GetRemote(name)
-	if err != nil {
-		return nil, err
-	}
-
-	return remote.Config(), nil
-}
-
-// HasRemote checks if a remote with the given name exists
-func (rh *RemoteHelper) HasRemote(name string) bool {
-	_, err := rh.repo.Remote(name)
-	return err == nil
-}

internal/git/rerere.go

@@ -1,286 +0,0 @@
-package git
-
-import (
-	"crypto/sha1"
-	"encoding/hex"
-	"fmt"
-	"io"
-	"os"
-	"path/filepath"
-	"strings"
-
-	"github.com/go-git/go-git/v5"
-)
-
-// RerereManager manages git rerere (reuse recorded resolution) functionality
-type RerereManager struct {
-	repo       *git.Repository
-	cachePath  string
-	enabled    bool
-	repoPath   string
-	conflictResolver *ConflictResolver
-}
-
-// NewRerereManager creates a new RerereManager instance
-func NewRerereManager(repo *git.Repository, onyxPath, repoPath string) *RerereManager {
-	cachePath := filepath.Join(onyxPath, "rerere_cache")
-
-	return &RerereManager{
-		repo:             repo,
-		cachePath:        cachePath,
-		enabled:          true,
-		repoPath:         repoPath,
-		conflictResolver: NewConflictResolver(repo, repoPath),
-	}
-}
-
-// Enable enables rerere functionality
-func (rm *RerereManager) Enable() {
-	rm.enabled = true
-}
-
-// Disable disables rerere functionality
-func (rm *RerereManager) Disable() {
-	rm.enabled = false
-}
-
-// IsEnabled returns whether rerere is enabled
-func (rm *RerereManager) IsEnabled() bool {
-	return rm.enabled
-}
-
-// RecordConflicts records current conflicts for future resolution
-func (rm *RerereManager) RecordConflicts() error {
-	if !rm.enabled {
-		return nil
-	}
-
-	conflicts, err := rm.conflictResolver.DetectConflicts()
-	if err != nil {
-		return fmt.Errorf("failed to detect conflicts: %w", err)
-	}
-
-	if len(conflicts) == 0 {
-		return nil
-	}
-
-	// For each conflict, create a cache entry
-	for _, conflict := range conflicts {
-		if err := rm.recordConflict(conflict); err != nil {
-			// Log error but continue with other conflicts
-			fmt.Fprintf(os.Stderr, "Warning: failed to record conflict for %s: %v\n", conflict.FilePath, err)
-		}
-	}
-
-	return nil
-}
-
-// recordConflict records a single conflict
-func (rm *RerereManager) recordConflict(conflict ConflictInfo) error {
-	// Read the conflicted file
-	fullPath := filepath.Join(rm.repoPath, conflict.FilePath)
-	content, err := os.ReadFile(fullPath)
-	if err != nil {
-		return fmt.Errorf("failed to read conflicted file: %w", err)
-	}
-
-	// Generate a unique ID for this conflict pattern
-	conflictID := rm.generateConflictID(content)
-
-	// Create cache directory for this conflict
-	conflictDir := filepath.Join(rm.cachePath, conflictID)
-	if err := os.MkdirAll(conflictDir, 0755); err != nil {
-		return fmt.Errorf("failed to create conflict cache directory: %w", err)
-	}
-
-	// Save the preimage (conflict state)
-	preimagePath := filepath.Join(conflictDir, "preimage")
-	if err := os.WriteFile(preimagePath, content, 0644); err != nil {
-		return fmt.Errorf("failed to write preimage: %w", err)
-	}
-
-	// Save metadata
-	metadataPath := filepath.Join(conflictDir, "metadata")
-	metadata := fmt.Sprintf("file=%s\nbase=%s\nours=%s\ntheirs=%s\n",
-		conflict.FilePath, conflict.BaseHash, conflict.OursHash, conflict.TheirsHash)
-	if err := os.WriteFile(metadataPath, []byte(metadata), 0644); err != nil {
-		return fmt.Errorf("failed to write metadata: %w", err)
-	}
-
-	return nil
-}
-
-// RecordResolution records the resolution for previously recorded conflicts
-func (rm *RerereManager) RecordResolution() error {
-	if !rm.enabled {
-		return nil
-	}
-
-	// Find all recorded conflicts
-	entries, err := os.ReadDir(rm.cachePath)
-	if err != nil {
-		if os.IsNotExist(err) {
-			return nil
-		}
-		return fmt.Errorf("failed to read rerere cache: %w", err)
-	}
-
-	for _, entry := range entries {
-		if !entry.IsDir() {
-			continue
-		}
-
-		conflictID := entry.Name()
-		if err := rm.recordResolutionForConflict(conflictID); err != nil {
-			// Log error but continue
-			fmt.Fprintf(os.Stderr, "Warning: failed to record resolution for %s: %v\n", conflictID, err)
-		}
-	}
-
-	return nil
-}
-
-// recordResolutionForConflict records the resolution for a specific conflict
-func (rm *RerereManager) recordResolutionForConflict(conflictID string) error {
-	conflictDir := filepath.Join(rm.cachePath, conflictID)
-
-	// Read metadata to get file path
-	metadataPath := filepath.Join(conflictDir, "metadata")
-	metadataContent, err := os.ReadFile(metadataPath)
-	if err != nil {
-		return fmt.Errorf("failed to read metadata: %w", err)
-	}
-
-	// Parse file path from metadata
-	filePath := ""
-	for _, line := range strings.Split(string(metadataContent), "\n") {
-		if strings.HasPrefix(line, "file=") {
-			filePath = strings.TrimPrefix(line, "file=")
-			break
-		}
-	}
-
-	if filePath == "" {
-		return fmt.Errorf("file path not found in metadata")
-	}
-
-	// Check if file still has conflicts
-	fullPath := filepath.Join(rm.repoPath, filePath)
-	if _, err := os.Stat(fullPath); os.IsNotExist(err) {
-		// File was deleted or doesn't exist, skip
-		return nil
-	}
-
-	hasConflicts, err := rm.conflictResolver.IsFileConflicted(filePath)
-	if err != nil {
-		return fmt.Errorf("failed to check if file is conflicted: %w", err)
-	}
-
-	if hasConflicts {
-		// Still has conflicts, not resolved yet
-		return nil
-	}
-
-	// Read the resolved content
-	resolvedContent, err := os.ReadFile(fullPath)
-	if err != nil {
-		return fmt.Errorf("failed to read resolved file: %w", err)
-	}
-
-	// Save the postimage (resolved state)
-	postimagePath := filepath.Join(conflictDir, "postimage")
-	if err := os.WriteFile(postimagePath, resolvedContent, 0644); err != nil {
-		return fmt.Errorf("failed to write postimage: %w", err)
-	}
-
-	return nil
-}
-
-// ApplyResolutions applies previously recorded resolutions to current conflicts
-func (rm *RerereManager) ApplyResolutions() (int, error) {
-	if !rm.enabled {
-		return 0, nil
-	}
-
-	conflicts, err := rm.conflictResolver.DetectConflicts()
-	if err != nil {
-		return 0, fmt.Errorf("failed to detect conflicts: %w", err)
-	}
-
-	appliedCount := 0
-
-	for _, conflict := range conflicts {
-		// Read the conflicted file
-		fullPath := filepath.Join(rm.repoPath, conflict.FilePath)
-		content, err := os.ReadFile(fullPath)
-		if err != nil {
-			continue
-		}
-
-		// Generate conflict ID
-		conflictID := rm.generateConflictID(content)
-
-		// Check if we have a resolution for this conflict
-		postimagePath := filepath.Join(rm.cachePath, conflictID, "postimage")
-		if _, err := os.Stat(postimagePath); os.IsNotExist(err) {
-			continue
-		}
-
-		// Apply the resolution
-		resolvedContent, err := os.ReadFile(postimagePath)
-		if err != nil {
-			continue
-		}
-
-		if err := os.WriteFile(fullPath, resolvedContent, 0644); err != nil {
-			continue
-		}
-
-		appliedCount++
-	}
-
-	return appliedCount, nil
-}
-
-// generateConflictID generates a unique ID for a conflict pattern
-func (rm *RerereManager) generateConflictID(content []byte) string {
-	// Normalize conflict content by removing variable parts
-	normalized := rm.normalizeConflict(content)
-
-	// Generate SHA1 hash
-	hash := sha1.New()
-	io.WriteString(hash, normalized)
-	return hex.EncodeToString(hash.Sum(nil))
-}
-
-// normalizeConflict normalizes conflict content for matching
-func (rm *RerereManager) normalizeConflict(content []byte) string {
-	// Convert to string
-	str := string(content)
-
-	// Remove commit hashes from conflict markers (they vary)
-	lines := strings.Split(str, "\n")
-	var normalized []string
-
-	for _, line := range lines {
-		if strings.HasPrefix(line, "<<<<<<<") {
-			normalized = append(normalized, "<<<<<<<")
-		} else if strings.HasPrefix(line, ">>>>>>>") {
-			normalized = append(normalized, ">>>>>>>")
-		} else {
-			normalized = append(normalized, line)
-		}
-	}
-
-	return strings.Join(normalized, "\n")
-}
-
-// ClearCache clears the rerere cache
-func (rm *RerereManager) ClearCache() error {
-	return os.RemoveAll(rm.cachePath)
-}
-
-// GetCachePath returns the path to the rerere cache
-func (rm *RerereManager) GetCachePath() string {
-	return rm.cachePath
-}

notes/checklist.md

@@ -1,49 +1,54 @@
-## Milestone 4: Synchronization and Remote Interaction ✓ COMPLETE
+## Milestone 3: Workstreams ✓ COMPLETE
 
-**Completion Date:** October 14, 2025
+### Workstream Data Model
-**Status:** All features implemented and tested
-**Development Method:** Dogfooded using Onyx itself
 
-### Rebase Engine ✓
+28. ✓ **Implement workstream storage** (`internal/storage/workstreams.go`)
+    - `LoadWorkstreams(path string) (*WorkstreamCollection, error)`
+    - `SaveWorkstreams(path string, collection *WorkstreamCollection) error`
 
-34. **Implement stacked rebase** (`internal/git/rebase.go`) ✓
+29. ✓ **Create workstream manager** (`internal/core/workstream_manager.go`)
-    - Implemented RebaseStack function
+    - `CreateWorkstream(name string, base string) error`
-    - Sequential rebase with conflict handling
+    - `GetCurrentWorkstream() (*Workstream, error)`
-    - Integration with rerere for automatic conflict resolution
+    - `SwitchWorkstream(name string) error`
-    - Support for rebase continuation and abort
+    - `ListWorkstreams() ([]*Workstream, error)`
+    - `AddCommitToWorkstream(sha, message string) error`
+    - `GetCurrentWorkstreamName() (string, error)`
 
-35. **Integrate rerere** (`internal/git/rerere.go`) ✓
+### Workstream Commands
-    - Configured rerere cache location (.onx/rerere_cache)
-    - Enabled rerere for rebase operations
-    - Implemented conflict detection and recording
-    - Apply recorded resolutions automatically
 
-36. **Create conflict resolution UI** (`internal/git/conflicts.go`) ✓
+30. ✓ **Implement onx new** (`internal/commands/new.go`)
-    - Detect merge conflicts via index stages
+    - Validates workstream name
-    - Present clear conflict markers with file paths
+    - Creates workstream entry
-    - Guide user through resolution process
+    - Sets as current workstream
-    - Record resolutions for rerere
+    - Updates workspace to base commit
+    - Logs to oplog with transaction wrapper
+    - Provides helpful next-step guidance
 
-### Sync and Push Commands ✓
+31. ✓ **Implement onx list** (`internal/commands/list.go`)
+    - Reads workstreams.json via storage layer
+    - Formats output with current indicator (*)
+    - Shows commit count per workstream
+    - Color-coded output for status (active=green, merged/abandoned/archived=gray)
+    - `--all` flag to show non-active workstreams
+    - Alias: `ls`
 
-37. **Implement onx sync** (`internal/commands/sync.go`) ✓
+32. ✓ **Implement onx switch** (`internal/commands/switch.go`)
-    - Begin oplog transaction for undo support
+    - Validates target workstream exists
-    - Fetch from remote (origin by default)
+    - Checkouts latest commit in target workstream
-    - Get workstream commit stack
+    - Updates current_workstream pointer
-    - Sequential rebase with rerere support
+    - Logs to oplog with transaction wrapper
-    - Handle and present conflicts clearly
+    - Shows helpful info about target workstream
-    - Update workstreams.json with new SHAs
-    - Finalize oplog transaction
 
-38. **Implement onx push** (`internal/commands/push.go`) ✓
+33. ✓ **Add workstream validation**
-    - Get all branches in current workstream
+    - Validates workstream names (alphanumeric, hyphens, underscores, slashes only)
-    - Push each workstream branch to remote
+    - Prevents duplicate workstream names
-    - Support for force push flag
+    - Prevents reserved names (HEAD, main, master, etc.)
-    - Progress reporting for each branch
+    - Integrated in `ValidateWorkstreamName()` function
-    - Clear summary of pushed branches
+
+### Integration & Refactoring
+
+- ✓ Refactored `onx save` to use WorkstreamManager
+- ✓ All commands properly wired in `cmd/onx/main.go`
+- ✓ All tests passing
+- ✓ Build successful
 
-39. **Add remote configuration** (`internal/git/remote.go`) ✓
-    - Read git remote configuration
-    - Support multiple remotes
-    - Default to "origin"
-    - Validate remote existence and URLs

notes/future.md

@@ -1,3 +1,58 @@
+## Milestone 4: Synchronization and Remote Interaction
+
+### Rebase Engine
+
+34. **Implement stacked rebase** (`internal/git/rebase.go`)
+    ```go
+    func RebaseStack(repo *Repository, stack []string, 
+        onto string) error {
+        // 1. Rebase first commit onto target
+        // 2. For each subsequent commit:
+        //    - Rebase onto previous
+        //    - Handle conflicts
+        // 3. Update all branch refs
+    }
+    ```
+
+35. **Integrate rerere** (`internal/git/rerere.go`)
+    - Configure rerere cache location (.onx/rerere_cache)
+    - Enable rerere for rebase operations
+    - Implement conflict detection
+    - Apply recorded resolutions automatically
+
+36. **Create conflict resolution UI** (`internal/git/conflicts.go`)
+    - Detect merge conflicts
+    - Present clear conflict markers
+    - Guide user through resolution
+    - Record resolution for rerere
+
+### Sync and Push Commands
+
+37. **Implement onx sync** (`internal/commands/sync.go`)
+    ```go
+    func Sync(repo *Repository) error {
+        // 1. Begin oplog transaction
+        // 2. Fetch from origin
+        // 3. Get workstream stack
+        // 4. Sequential rebase with rerere
+        // 5. Handle conflicts
+        // 6. Update workstreams.json
+        // 7. Finalize oplog transaction
+    }
+    ```
+
+38. **Implement onx push** (`internal/commands/push.go`)
+    - Get all branches in current workstream
+    - Push each branch to remote
+    - Handle authentication (SSH/HTTPS)
+    - Report progress for each branch
+
+39. **Add remote configuration**
+    - Read git remote configuration
+    - Support multiple remotes
+    - Default to "origin"
+    - Validate remote existence
+
 ## Testing Infrastructure
 
 40. **Create test utilities** (`internal/testutil/`)