Step 5: Checkpoint and Status.

Checkpoint re-hashes all tracked files, stores changed blobs, and
updates per-file timestamps only when content changes. Missing files
are skipped gracefully. Status compares each tracked entry against
the filesystem and reports ok/modified/missing.

CLI: sgard checkpoint [-m message], sgard status.
4 new tests (changed file, unchanged file, missing file, status).

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

PROGRESS.md

@@ -7,7 +7,7 @@ ARCHITECTURE.md for design details.
 
 ## Current Status
 
-**Phase:** Steps 1–4 complete. Ready for Step 5 (Checkpoint and Status).
+**Phase:** Steps 1–5 complete. Ready for Step 6 (Restore).
 
 **Last updated:** 2026-03-23
 
@@ -24,6 +24,9 @@ ARCHITECTURE.md for design details.
 - **Step 4: Garden Core — Init and Add** — `Garden` struct tying manifest +
   store, `Init()`, `Open()`, `Add()` handling files/dirs/symlinks, `HashFile()`,
   tilde path conversion, CLI `init` and `add` commands. 8 tests.
+- **Step 5: Checkpoint and Status** — `Checkpoint()` re-hashes all tracked files,
+  stores changed blobs, updates timestamps. `Status()` reports ok/modified/missing
+  per entry. CLI `checkpoint` (with `-m` flag) and `status` commands. 4 tests.
 
 ## In Progress
 
@@ -31,7 +34,7 @@ ARCHITECTURE.md for design details.
 
 ## Up Next
 
-Step 5: Checkpoint and Status.
+Step 6: Restore.
 
 ## Known Issues / Decisions Deferred
 
@@ -49,3 +52,4 @@ Step 5: Checkpoint and Status.
 | 2026-03-23 | 2 | Manifest package complete. Structs, Load/Save with atomic write, full test suite. |
 | 2026-03-23 | 3 | Store package complete. Content-addressable blob store, 11 tests. |
 | 2026-03-23 | 4 | Garden core complete. Init, Open, Add with file/dir/symlink support, CLI commands. 8 tests. |
+| 2026-03-23 | 5 | Checkpoint and Status complete. Re-hash, store changed blobs, status reporting. 4 tests. |

PROJECT_PLAN.md

@@ -54,10 +54,10 @@ Depends on Steps 2 and 3.
 
 Depends on Step 4.
 
-- [ ] `garden/garden.go`: `Checkpoint(message string) error` — re-hash all tracked files, store changed blobs, update manifest timestamps
+- [x] `garden/garden.go`: `Checkpoint(message string) error` — re-hash all tracked files, store changed blobs, update manifest timestamps
-- [ ] `garden/garden.go`: `Status() ([]FileStatus, error)` — compare current hashes to manifest; report modified/missing/ok
+- [x] `garden/garden.go`: `Status() ([]FileStatus, error)` — compare current hashes to manifest; report modified/missing/ok
-- [ ] `garden/garden_test.go`: checkpoint detects changed files, status reports correctly
+- [x] `garden/garden_test.go`: checkpoint detects changed files, status reports correctly
-- [ ] Wire up CLI: `cmd/sgard/checkpoint.go`, `cmd/sgard/status.go`
+- [x] Wire up CLI: `cmd/sgard/checkpoint.go`, `cmd/sgard/status.go`
 
 ## Step 6: Restore
 

cmd/sgard/checkpoint.go

@@ -0,0 +1,33 @@
+package main
+
+import (
+	"fmt"
+
+	"github.com/kisom/sgard/garden"
+	"github.com/spf13/cobra"
+)
+
+var checkpointMessage string
+
+var checkpointCmd = &cobra.Command{
+	Use:   "checkpoint",
+	Short: "Re-hash all tracked files and update the manifest",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		g, err := garden.Open(repoFlag)
+		if err != nil {
+			return err
+		}
+
+		if err := g.Checkpoint(checkpointMessage); err != nil {
+			return err
+		}
+
+		fmt.Println("Checkpoint complete.")
+		return nil
+	},
+}
+
+func init() {
+	checkpointCmd.Flags().StringVarP(&checkpointMessage, "message", "m", "", "checkpoint message")
+	rootCmd.AddCommand(checkpointCmd)
+}

cmd/sgard/status.go

@@ -0,0 +1,34 @@
+package main
+
+import (
+	"fmt"
+
+	"github.com/kisom/sgard/garden"
+	"github.com/spf13/cobra"
+)
+
+var statusCmd = &cobra.Command{
+	Use:   "status",
+	Short: "Show status of tracked files: ok, modified, or missing",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		g, err := garden.Open(repoFlag)
+		if err != nil {
+			return err
+		}
+
+		statuses, err := g.Status()
+		if err != nil {
+			return err
+		}
+
+		for _, s := range statuses {
+			fmt.Printf("%-10s %s\n", s.State, s.Path)
+		}
+
+		return nil
+	},
+}
+
+func init() {
+	rootCmd.AddCommand(statusCmd)
+}

garden/garden.go

@@ -148,6 +148,127 @@ func (g *Garden) Add(paths []string) error {
 	return nil
 }
 
+// FileStatus reports the state of a tracked entry relative to the filesystem.
+type FileStatus struct {
+	Path  string // tilde path from manifest
+	State string // "ok", "modified", "missing"
+}
+
+// Checkpoint re-hashes all tracked files, stores any changed blobs, and
+// updates the manifest timestamps. The optional message is recorded in
+// the manifest.
+func (g *Garden) Checkpoint(message string) error {
+	now := time.Now().UTC()
+
+	for i := range g.manifest.Files {
+		entry := &g.manifest.Files[i]
+
+		abs, err := ExpandTildePath(entry.Path)
+		if err != nil {
+			return fmt.Errorf("expanding path %s: %w", entry.Path, err)
+		}
+
+		info, err := os.Lstat(abs)
+		if err != nil {
+			// File is missing — leave the manifest entry as-is so status
+			// can report it. Don't fail the whole checkpoint.
+			continue
+		}
+
+		entry.Mode = fmt.Sprintf("%04o", info.Mode().Perm())
+
+		switch entry.Type {
+		case "file":
+			data, err := os.ReadFile(abs)
+			if err != nil {
+				return fmt.Errorf("reading %s: %w", abs, err)
+			}
+			hash, err := g.store.Write(data)
+			if err != nil {
+				return fmt.Errorf("storing blob for %s: %w", abs, err)
+			}
+			if hash != entry.Hash {
+				entry.Hash = hash
+				entry.Updated = now
+			}
+
+		case "link":
+			target, err := os.Readlink(abs)
+			if err != nil {
+				return fmt.Errorf("reading symlink %s: %w", abs, err)
+			}
+			if target != entry.Target {
+				entry.Target = target
+				entry.Updated = now
+			}
+
+		case "directory":
+			// Nothing to hash; just update mode (already done above).
+		}
+	}
+
+	g.manifest.Updated = now
+	g.manifest.Message = message
+	if err := g.manifest.Save(g.manifestPath); err != nil {
+		return fmt.Errorf("saving manifest: %w", err)
+	}
+
+	return nil
+}
+
+// Status compares each tracked entry against the current filesystem state
+// and returns a status for each.
+func (g *Garden) Status() ([]FileStatus, error) {
+	var results []FileStatus
+
+	for i := range g.manifest.Files {
+		entry := &g.manifest.Files[i]
+
+		abs, err := ExpandTildePath(entry.Path)
+		if err != nil {
+			return nil, fmt.Errorf("expanding path %s: %w", entry.Path, err)
+		}
+
+		_, err = os.Lstat(abs)
+		if os.IsNotExist(err) {
+			results = append(results, FileStatus{Path: entry.Path, State: "missing"})
+			continue
+		}
+		if err != nil {
+			return nil, fmt.Errorf("stat %s: %w", abs, err)
+		}
+
+		switch entry.Type {
+		case "file":
+			hash, err := HashFile(abs)
+			if err != nil {
+				return nil, fmt.Errorf("hashing %s: %w", abs, err)
+			}
+			if hash != entry.Hash {
+				results = append(results, FileStatus{Path: entry.Path, State: "modified"})
+			} else {
+				results = append(results, FileStatus{Path: entry.Path, State: "ok"})
+			}
+
+		case "link":
+			target, err := os.Readlink(abs)
+			if err != nil {
+				return nil, fmt.Errorf("reading symlink %s: %w", abs, err)
+			}
+			if target != entry.Target {
+				results = append(results, FileStatus{Path: entry.Path, State: "modified"})
+			} else {
+				results = append(results, FileStatus{Path: entry.Path, State: "ok"})
+			}
+
+		case "directory":
+			results = append(results, FileStatus{Path: entry.Path, State: "ok"})
+		}
+	}
+
+	return results, nil
+}
+
 // findEntry returns the entry for the given tilde path, or nil if not found.
 func (g *Garden) findEntry(tildePath string) *manifest.Entry {
 	for i := range g.manifest.Files {

garden/garden_test.go

@@ -218,6 +218,179 @@ func TestHashFile(t *testing.T) {
 	}
 }
 
+func TestCheckpointDetectsChanges(t *testing.T) {
+	root := t.TempDir()
+	repoDir := filepath.Join(root, "repo")
+
+	g, err := Init(repoDir)
+	if err != nil {
+		t.Fatalf("Init: %v", err)
+	}
+
+	testFile := filepath.Join(root, "testfile")
+	if err := os.WriteFile(testFile, []byte("original"), 0o644); err != nil {
+		t.Fatalf("writing test file: %v", err)
+	}
+
+	if err := g.Add([]string{testFile}); err != nil {
+		t.Fatalf("Add: %v", err)
+	}
+
+	origHash := g.manifest.Files[0].Hash
+
+	// Modify the file.
+	if err := os.WriteFile(testFile, []byte("modified"), 0o644); err != nil {
+		t.Fatalf("modifying test file: %v", err)
+	}
+
+	if err := g.Checkpoint("test checkpoint"); err != nil {
+		t.Fatalf("Checkpoint: %v", err)
+	}
+
+	if g.manifest.Files[0].Hash == origHash {
+		t.Error("checkpoint did not update hash for modified file")
+	}
+	if g.manifest.Message != "test checkpoint" {
+		t.Errorf("expected message 'test checkpoint', got %q", g.manifest.Message)
+	}
+
+	// Verify new blob exists in store.
+	if !g.store.Exists(g.manifest.Files[0].Hash) {
+		t.Error("new blob not found in store")
+	}
+
+	// Verify manifest persisted.
+	g2, err := Open(repoDir)
+	if err != nil {
+		t.Fatalf("re-Open: %v", err)
+	}
+	if g2.manifest.Files[0].Hash == origHash {
+		t.Error("persisted manifest still has old hash")
+	}
+}
+
+func TestCheckpointUnchangedFile(t *testing.T) {
+	root := t.TempDir()
+	repoDir := filepath.Join(root, "repo")
+
+	g, err := Init(repoDir)
+	if err != nil {
+		t.Fatalf("Init: %v", err)
+	}
+
+	testFile := filepath.Join(root, "testfile")
+	if err := os.WriteFile(testFile, []byte("same"), 0o644); err != nil {
+		t.Fatalf("writing test file: %v", err)
+	}
+
+	if err := g.Add([]string{testFile}); err != nil {
+		t.Fatalf("Add: %v", err)
+	}
+
+	origHash := g.manifest.Files[0].Hash
+	origUpdated := g.manifest.Files[0].Updated
+
+	if err := g.Checkpoint(""); err != nil {
+		t.Fatalf("Checkpoint: %v", err)
+	}
+
+	if g.manifest.Files[0].Hash != origHash {
+		t.Error("hash should not change for unmodified file")
+	}
+	if !g.manifest.Files[0].Updated.Equal(origUpdated) {
+		t.Error("entry timestamp should not change for unmodified file")
+	}
+}
+
+func TestCheckpointMissingFileSkipped(t *testing.T) {
+	root := t.TempDir()
+	repoDir := filepath.Join(root, "repo")
+
+	g, err := Init(repoDir)
+	if err != nil {
+		t.Fatalf("Init: %v", err)
+	}
+
+	testFile := filepath.Join(root, "testfile")
+	if err := os.WriteFile(testFile, []byte("data"), 0o644); err != nil {
+		t.Fatalf("writing test file: %v", err)
+	}
+
+	if err := g.Add([]string{testFile}); err != nil {
+		t.Fatalf("Add: %v", err)
+	}
+
+	// Remove the file before checkpoint.
+	os.Remove(testFile)
+
+	// Checkpoint should not fail.
+	if err := g.Checkpoint(""); err != nil {
+		t.Fatalf("Checkpoint should not fail for missing file: %v", err)
+	}
+}
+
+func TestStatusReportsCorrectly(t *testing.T) {
+	root := t.TempDir()
+	repoDir := filepath.Join(root, "repo")
+
+	g, err := Init(repoDir)
+	if err != nil {
+		t.Fatalf("Init: %v", err)
+	}
+
+	// Create and add two files.
+	okFile := filepath.Join(root, "okfile")
+	if err := os.WriteFile(okFile, []byte("unchanged"), 0o644); err != nil {
+		t.Fatalf("writing ok file: %v", err)
+	}
+	modFile := filepath.Join(root, "modfile")
+	if err := os.WriteFile(modFile, []byte("original"), 0o644); err != nil {
+		t.Fatalf("writing mod file: %v", err)
+	}
+	missingFile := filepath.Join(root, "missingfile")
+	if err := os.WriteFile(missingFile, []byte("will vanish"), 0o644); err != nil {
+		t.Fatalf("writing missing file: %v", err)
+	}
+
+	if err := g.Add([]string{okFile, modFile, missingFile}); err != nil {
+		t.Fatalf("Add: %v", err)
+	}
+
+	// Modify one file, remove another.
+	if err := os.WriteFile(modFile, []byte("changed"), 0o644); err != nil {
+		t.Fatalf("modifying file: %v", err)
+	}
+	os.Remove(missingFile)
+
+	statuses, err := g.Status()
+	if err != nil {
+		t.Fatalf("Status: %v", err)
+	}
+
+	if len(statuses) != 3 {
+		t.Fatalf("expected 3 statuses, got %d", len(statuses))
+	}
+
+	stateMap := make(map[string]string)
+	for _, s := range statuses {
+		stateMap[s.Path] = s.State
+	}
+
+	okPath := toTildePath(okFile)
+	modPath := toTildePath(modFile)
+	missingPath := toTildePath(missingFile)
+
+	if stateMap[okPath] != "ok" {
+		t.Errorf("okfile: expected ok, got %s", stateMap[okPath])
+	}
+	if stateMap[modPath] != "modified" {
+		t.Errorf("modfile: expected modified, got %s", stateMap[modPath])
+	}
+	if stateMap[missingPath] != "missing" {
+		t.Errorf("missingfile: expected missing, got %s", stateMap[missingPath])
+	}
+}
+
 func TestExpandTildePath(t *testing.T) {
 	home, err := os.UserHomeDir()
 	if err != nil {