feat: own the branch synchronization engine

Replace the external hub sync dependency with an attributed internal implementation that fetches and updates branches independently. Allow dirty repositories while protecting affected checked-out branches, retain all-clean strict mode, add real-remote safety tests, and update the CLI, TUI, JSON output, version, and documentation.

main.go

@@ -3,7 +3,6 @@ package main
 import (
 	"bufio"
 	"bytes"
-	"context"
 	"encoding/json"
 	"errors"
 	"flag"
@@ -19,7 +18,7 @@ import (
 	"time"
 )
 
-const version = "0.2.0"
+const version = "0.3.0"
 
 var defaultSkippedDirs = map[string]bool{
 	".cache": true, ".claude": true, ".codex": true, ".git": true, ".next": true, ".pnpm-store": true,
@@ -57,11 +56,12 @@ type repo struct {
 }
 
 type syncResult struct {
-	Path     string `json:"path"`
-	Success  bool   `json:"success"`
-	Skipped  bool   `json:"skipped"`
-	Message  string `json:"message,omitempty"`
-	Duration string `json:"duration,omitempty"`
+	Path     string             `json:"path"`
+	Success  bool               `json:"success"`
+	Skipped  bool               `json:"skipped"`
+	Message  string             `json:"message,omitempty"`
+	Duration string             `json:"duration,omitempty"`
+	Branches []branchSyncResult `json:"branches,omitempty"`
 }
 
 func main() {
@@ -130,21 +130,17 @@ func run(args []string, stdin io.Reader, stdout, stderr io.Writer) int {
 		return 0
 	}
 
-	if _, err := exec.LookPath("hub"); err != nil {
-		fmt.Fprintln(stderr, "hub is required for sync but was not found on PATH")
-		return 1
-	}
 	if !opts.json {
 		printScan(stdout, root, repos)
 	}
 	eligible := eligibleCount(repos)
-	blocked := blockedCount(repos)
 	if eligible == 0 {
 		fmt.Fprintln(stderr, "nothing to sync: every repository is blocked")
 		return 3
 	}
-	if opts.strict && blocked > 0 {
-		fmt.Fprintf(stderr, "strict mode: refusing to sync because %d repositories are blocked\n", blocked)
+	strictUnsafe := strictUnsafeCount(repos)
+	if opts.strict && strictUnsafe > 0 {
+		fmt.Fprintf(stderr, "strict mode: refusing to sync because %d repositories are blocked or dirty\n", strictUnsafe)
 		return 3
 	}
 	if !opts.yes {
@@ -152,7 +148,7 @@ func run(args []string, stdin io.Reader, stdout, stderr io.Writer) int {
 			fmt.Fprintln(stderr, "refusing to sync without confirmation; pass --yes in non-interactive use")
 			return 2
 		}
-		fmt.Fprintf(stdout, "\nRun hub sync in %d clean repositories? hub may delete local branches it considers merged. [y/N] ", eligible)
+		fmt.Fprintf(stdout, "\nSynchronize branches in %d repositories? Merged branches whose upstream was deleted may be removed. [y/N] ", eligible)
 		answer, _ := bufio.NewReader(stdin).ReadString('\n')
 		answer = strings.ToLower(strings.TrimSpace(answer))
 		if answer != "y" && answer != "yes" {
@@ -161,7 +157,7 @@ func run(args []string, stdin io.Reader, stdout, stderr io.Writer) int {
 		}
 	}
 
-	results := syncAll(root, repos, opts.jobs, opts.timeout, stdout, opts.json)
+	results := syncAll(root, repos, opts.jobs, opts.timeout, stdout, opts.json, opts.strict)
 	if opts.json {
 		writeJSON(stdout, results)
 	} else {
@@ -190,10 +186,10 @@ func parseFlags(command string, args []string, stderr io.Writer) (options, error
 	fs.Var(&opts.exclusions, "exclude", "directory name or root-relative path to skip (repeatable)")
 	if command == "sync" {
 		fs.BoolVar(&opts.yes, "yes", false, "apply without an interactive confirmation")
-		fs.BoolVar(&opts.strict, "strict", false, "abort the entire run if any repository is blocked")
+		fs.BoolVar(&opts.strict, "strict", false, "abort the entire run if any repository is blocked or dirty")
 	}
 	if command == "sync" || command == "tui" {
-		fs.DurationVar(&opts.timeout, "timeout", opts.timeout, "timeout for each hub sync")
+		fs.DurationVar(&opts.timeout, "timeout", opts.timeout, "timeout for each repository sync")
 	}
 	fs.Usage = func() { usage(stderr) }
 	if err := fs.Parse(args); err != nil {
@@ -218,7 +214,7 @@ func parseFlags(command string, args []string, stderr io.Writer) (options, error
 }
 
 func usage(w io.Writer) {
-	fmt.Fprintln(w, `stack-sync safely runs hub sync across a directory tree.
+	fmt.Fprintln(w, `stack-sync safely synchronizes Git branches across a directory tree.
 
 Usage:
   stack-sync [scan] [options]
@@ -228,13 +224,14 @@ Usage:
 
 Commands:
   scan   Discover repositories and report whether each is safe to sync (default)
-  sync   Scan, confirm, re-check safety, then run hub sync in eligible repositories
+  sync   Scan, confirm, re-check safety, then sync branches in eligible repositories
   tui    Interactively review, select, and sync repositories
 
 Safety:
-  Repositories with edits, untracked files, detached HEADs, no remotes, or an
-  in-progress Git operation are never synced. Untracked nested repositories do
-  not falsely dirty their parent. stack-sync never stashes, resets, or commits.
+  Dirty worktrees are reported but remain eligible: their checked-out branch is
+  protected while safe inactive branches are synchronized. Detached HEADs,
+  repositories without remotes, and in-progress Git operations remain blocked.
+  stack-sync never stashes, resets, cleans, or commits.
 
 Use "stack-sync <command> -h" for command options.`)
 }
@@ -336,9 +333,6 @@ func inspect(root, path string, allRepos []string) repo {
 		}
 		r.Dirty = append(r.Dirty, change.code+" "+change.path)
 	}
-	if len(r.Dirty) > 0 {
-		setBlock(&r, fmt.Sprintf("dirty worktree (%d changes)", len(r.Dirty)))
-	}
 	r.Eligible = r.BlockReason == ""
 	return r
 }
@@ -422,11 +416,11 @@ func gitBytes(path string, args ...string) ([]byte, error) {
 	return cmd.Output()
 }
 
-func syncAll(root string, repos []repo, jobs int, timeout time.Duration, stdout io.Writer, quiet bool) []syncResult {
-	return syncSelected(root, repos, repos, jobs, timeout, stdout, quiet)
+func syncAll(root string, repos []repo, jobs int, timeout time.Duration, stdout io.Writer, quiet, strict bool) []syncResult {
+	return syncSelected(root, repos, repos, jobs, timeout, stdout, quiet, strict)
 }
 
-func syncSelected(root string, repos, workspaceRepos []repo, jobs int, timeout time.Duration, stdout io.Writer, quiet bool) []syncResult {
+func syncSelected(root string, repos, workspaceRepos []repo, jobs int, timeout time.Duration, stdout io.Writer, quiet, strict bool) []syncResult {
 	type item struct {
 		index int
 		repo  repo
@@ -456,22 +450,18 @@ func syncSelected(root string, repos, workspaceRepos []repo, jobs int, timeout t
 					results[next.index] = syncResult{Path: r.RelativePath, Skipped: true, Message: "pre-sync recheck: " + fresh.BlockReason}
 					continue
 				}
+				if strict && len(fresh.Dirty) > 0 {
+					results[next.index] = syncResult{Path: r.RelativePath, Skipped: true, Message: fmt.Sprintf("pre-sync recheck: dirty worktree (%d changes)", len(fresh.Dirty))}
+					continue
+				}
 				if !quiet {
 					outputMu.Lock()
 					fmt.Fprintf(stdout, "\nSTART  %s (%s)\n", r.RelativePath, r.Branch)
 					outputMu.Unlock()
 				}
 				started := time.Now()
-				ctx, cancel := context.WithTimeout(context.Background(), timeout)
-				cmd := exec.CommandContext(ctx, "hub", "sync", "--color=never")
-				cmd.Dir = r.Path
-				combined, err := cmd.CombinedOutput()
-				cancel()
-				message := strings.TrimSpace(string(combined))
-				if ctx.Err() == context.DeadlineExceeded {
-					err = ctx.Err()
-					message = "timed out after " + timeout.String()
-				}
+				report, err := syncRepository(r.Path, timeout, len(fresh.Dirty) > 0, fresh.NestedRepoEntries)
+				message := report.Message
 				duration := time.Since(started).Round(time.Millisecond).String()
 				if !quiet {
 					outputMu.Lock()
@@ -488,7 +478,7 @@ func syncSelected(root string, repos, workspaceRepos []repo, jobs int, timeout t
 				if err != nil && message == "" {
 					message = err.Error()
 				}
-				results[next.index] = syncResult{Path: r.RelativePath, Success: err == nil, Message: message, Duration: duration}
+				results[next.index] = syncResult{Path: r.RelativePath, Success: err == nil, Message: message, Duration: duration, Branches: report.Branches}
 			}
 		}()
 	}
@@ -513,6 +503,8 @@ func printScan(w io.Writer, root string, repos []repo) {
 		status := "ready"
 		if !r.Eligible {
 			status = "BLOCKED: " + r.BlockReason
+		} else if len(r.Dirty) > 0 {
+			status = fmt.Sprintf("ready; dirty worktree (%d changes), checked-out branch protected", len(r.Dirty))
 		}
 		if len(r.NestedRepoEntries) > 0 {
 			status += fmt.Sprintf("; %d nested repo path(s) ignored", len(r.NestedRepoEntries))
@@ -555,6 +547,15 @@ func eligibleCount(repos []repo) int {
 	return n
 }
 func blockedCount(repos []repo) int { return len(repos) - eligibleCount(repos) }
+func strictUnsafeCount(repos []repo) int {
+	n := 0
+	for _, r := range repos {
+		if !r.Eligible || len(r.Dirty) > 0 {
+			n++
+		}
+	}
+	return n
+}
 func writeJSON(w io.Writer, value any) {
 	enc := json.NewEncoder(w)
 	enc.SetIndent("", "  ")