Step 8: Polish — lint, clock abstraction, e2e test.

- golangci-lint config with errcheck, govet, staticcheck, errorlint
- Fix all lint issues (unchecked error returns in cleanup paths, De Morgan)
- Inject jonboulle/clockwork into Garden for deterministic timestamps
- Add manifest.NewWithTime() for clock-aware initialization
- E2e lifecycle test: init → add → checkpoint → modify → status → restore → verify
- Update CLAUDE.md, PROJECT_PLAN.md, PROGRESS.md

Phase 1 (local) is now complete. All 9 CLI commands implemented and tested.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

garden/e2e_test.go

@@ -0,0 +1,116 @@
+package garden
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/jonboulle/clockwork"
+)
+
+// TestE2E exercises the full lifecycle: init → add → checkpoint → modify →
+// status → restore → verify.
+func TestE2E(t *testing.T) {
+	root := t.TempDir()
+	repoDir := filepath.Join(root, "repo")
+
+	// Use a fake clock so timestamps are deterministic.
+	fakeClock := clockwork.NewFakeClockAt(time.Date(2026, 1, 1, 0, 0, 0, 0, time.UTC))
+
+	// 1. Init
+	g, err := Init(repoDir)
+	if err != nil {
+		t.Fatalf("Init: %v", err)
+	}
+	g.SetClock(fakeClock)
+
+	// 2. Create and add files.
+	bashrc := filepath.Join(root, "bashrc")
+	gitconfig := filepath.Join(root, "gitconfig")
+	if err := os.WriteFile(bashrc, []byte("export PS1='$ '\n"), 0o644); err != nil {
+		t.Fatalf("writing bashrc: %v", err)
+	}
+	if err := os.WriteFile(gitconfig, []byte("[user]\n\tname = test\n"), 0o644); err != nil {
+		t.Fatalf("writing gitconfig: %v", err)
+	}
+
+	if err := g.Add([]string{bashrc, gitconfig}); err != nil {
+		t.Fatalf("Add: %v", err)
+	}
+
+	if len(g.manifest.Files) != 2 {
+		t.Fatalf("expected 2 entries, got %d", len(g.manifest.Files))
+	}
+
+	// 3. Checkpoint.
+	fakeClock.Advance(time.Hour)
+	if err := g.Checkpoint("initial checkpoint"); err != nil {
+		t.Fatalf("Checkpoint: %v", err)
+	}
+
+	if g.manifest.Message != "initial checkpoint" {
+		t.Errorf("expected message 'initial checkpoint', got %q", g.manifest.Message)
+	}
+
+	// 4. Modify a file.
+	if err := os.WriteFile(bashrc, []byte("export PS1='> '\n"), 0o644); err != nil {
+		t.Fatalf("modifying bashrc: %v", err)
+	}
+
+	// 5. Status — should detect modification.
+	statuses, err := g.Status()
+	if err != nil {
+		t.Fatalf("Status: %v", err)
+	}
+
+	stateMap := make(map[string]string)
+	for _, s := range statuses {
+		stateMap[s.Path] = s.State
+	}
+
+	bashrcPath := toTildePath(bashrc)
+	gitconfigPath := toTildePath(gitconfig)
+
+	if stateMap[bashrcPath] != "modified" {
+		t.Errorf("bashrc should be modified, got %s", stateMap[bashrcPath])
+	}
+	if stateMap[gitconfigPath] != "ok" {
+		t.Errorf("gitconfig should be ok, got %s", stateMap[gitconfigPath])
+	}
+
+	// 6. Restore — force to overwrite modified file.
+	if err := g.Restore([]string{bashrc}, true, nil); err != nil {
+		t.Fatalf("Restore: %v", err)
+	}
+
+	got, err := os.ReadFile(bashrc)
+	if err != nil {
+		t.Fatalf("reading restored bashrc: %v", err)
+	}
+	if string(got) != "export PS1='$ '\n" {
+		t.Errorf("bashrc not restored correctly, got %q", got)
+	}
+
+	// 7. Status after restore — should be ok.
+	statuses, err = g.Status()
+	if err != nil {
+		t.Fatalf("Status after restore: %v", err)
+	}
+	for _, s := range statuses {
+		if s.State != "ok" {
+			t.Errorf("after restore, %s should be ok, got %s", s.Path, s.State)
+		}
+	}
+
+	// 8. Verify — all blobs should be intact.
+	results, err := g.Verify()
+	if err != nil {
+		t.Fatalf("Verify: %v", err)
+	}
+	for _, r := range results {
+		if !r.OK {
+			t.Errorf("verify failed for %s: %s", r.Path, r.Detail)
+		}
+	}
+}

garden/garden.go

@@ -10,6 +10,7 @@ import (
 	"strings"
 	"time"
 
+	"github.com/jonboulle/clockwork"
 	"github.com/kisom/sgard/manifest"
 	"github.com/kisom/sgard/store"
 )
@@ -20,6 +21,7 @@ type Garden struct {
 	store        *store.Store
 	root         string // repository root directory
 	manifestPath string // path to manifest.yaml
+	clock        clockwork.Clock
 }
 
 // Init creates a new sgard repository at root. It creates the directory
@@ -44,7 +46,8 @@ func Init(root string) (*Garden, error) {
 		return nil, fmt.Errorf("creating store: %w", err)
 	}
 
-	m := manifest.New()
+	clk := clockwork.NewRealClock()
+	m := manifest.NewWithTime(clk.Now().UTC())
 	if err := m.Save(manifestPath); err != nil {
 		return nil, fmt.Errorf("saving initial manifest: %w", err)
 	}
@@ -54,6 +57,7 @@ func Init(root string) (*Garden, error) {
 		store:        s,
 		root:         absRoot,
 		manifestPath: manifestPath,
+		clock:        clk,
 	}, nil
 }
 
@@ -80,14 +84,20 @@ func Open(root string) (*Garden, error) {
 		store:        s,
 		root:         absRoot,
 		manifestPath: manifestPath,
+		clock:        clockwork.NewRealClock(),
 	}, nil
 }
 
+// SetClock replaces the clock used for timestamps. Intended for testing.
+func (g *Garden) SetClock(c clockwork.Clock) {
+	g.clock = c
+}
+
 // Add tracks new files, directories, or symlinks. Each path is resolved
 // to an absolute path, inspected for its type, and added to the manifest.
 // Regular files are hashed and stored in the blob store.
 func (g *Garden) Add(paths []string) error {
-	now := time.Now().UTC()
+	now := g.clock.Now().UTC()
 
 	for _, p := range paths {
 		abs, err := filepath.Abs(p)
@@ -159,7 +169,7 @@ type FileStatus struct {
 // updates the manifest timestamps. The optional message is recorded in
 // the manifest.
 func (g *Garden) Checkpoint(message string) error {
-	now := time.Now().UTC()
+	now := g.clock.Now().UTC()
 
 	for i := range g.manifest.Files {
 		entry := &g.manifest.Files[i]
@@ -359,7 +369,7 @@ func (g *Garden) restoreFile(abs string, entry *manifest.Entry) error {
 
 func restoreLink(abs string, entry *manifest.Entry) error {
 	// Remove existing file/link at the target path so we can create the symlink.
-	os.Remove(abs)
+	_ = os.Remove(abs)
 
 	if err := os.Symlink(entry.Target, abs); err != nil {
 		return fmt.Errorf("creating symlink %s -> %s: %w", abs, entry.Target, err)

garden/garden_test.go

@@ -321,7 +321,7 @@ func TestCheckpointMissingFileSkipped(t *testing.T) {
 	}
 
 	// Remove the file before checkpoint.
-	os.Remove(testFile)
+	_ = os.Remove(testFile)
 
 	// Checkpoint should not fail.
 	if err := g.Checkpoint(""); err != nil {
@@ -360,7 +360,7 @@ func TestStatusReportsCorrectly(t *testing.T) {
 	if err := os.WriteFile(modFile, []byte("changed"), 0o644); err != nil {
 		t.Fatalf("modifying file: %v", err)
 	}
-	os.Remove(missingFile)
+	_ = os.Remove(missingFile)
 
 	statuses, err := g.Status()
 	if err != nil {
@@ -412,7 +412,7 @@ func TestRestoreFile(t *testing.T) {
 	}
 
 	// Delete the file, then restore it.
-	os.Remove(testFile)
+	_ = os.Remove(testFile)
 
 	if err := g.Restore(nil, true, nil); err != nil {
 		t.Fatalf("Restore: %v", err)
@@ -445,7 +445,7 @@ func TestRestorePermissions(t *testing.T) {
 		t.Fatalf("Add: %v", err)
 	}
 
-	os.Remove(testFile)
+	_ = os.Remove(testFile)
 
 	if err := g.Restore(nil, true, nil); err != nil {
 		t.Fatalf("Restore: %v", err)
@@ -482,7 +482,7 @@ func TestRestoreSymlink(t *testing.T) {
 		t.Fatalf("Add: %v", err)
 	}
 
-	os.Remove(link)
+	_ = os.Remove(link)
 
 	if err := g.Restore(nil, true, nil); err != nil {
 		t.Fatalf("Restore: %v", err)
@@ -520,7 +520,7 @@ func TestRestoreCreatesParentDirs(t *testing.T) {
 	}
 
 	// Remove the entire directory tree.
-	os.RemoveAll(filepath.Join(root, "a"))
+	_ = os.RemoveAll(filepath.Join(root, "a"))
 
 	if err := g.Restore(nil, true, nil); err != nil {
 		t.Fatalf("Restore: %v", err)
@@ -557,8 +557,8 @@ func TestRestoreSelectivePaths(t *testing.T) {
 		t.Fatalf("Add: %v", err)
 	}
 
-	os.Remove(file1)
-	os.Remove(file2)
+	_ = os.Remove(file1)
+	_ = os.Remove(file2)
 
 	// Restore only file1.
 	if err := g.Restore([]string{file1}, true, nil); err != nil {