Re-vendor the canonical files from sneak/prompts at dd4027b (closes #213)

Linting and testing become the lint and test phases of the Dockerfile,
and the build stage depends on both. Dockerfile.lint, CHECK_EPOCH and
the tests that checked them are removed. Every docker build in script/
passes --no-cache, and script/cibuild runs script/bootstrap first, which
now fetches apt package lists so a fresh CI runner can install Go. The
image takes its version from the VERSION build arg or git describe, dev
without .git, and still stamps the commit and its date. This repo's own
entries follow the canonical content in .gitignore and .editorconfig.
The golangci-lint v2.14.0 findings are fixed in the code. The rules in
CLAUDE.md move into AGENTS.md. IsDevVersion now counts "unknown".

Model: opus-5-5

.editorconfig

@@ -10,3 +10,6 @@ insert_final_newline = true
 
 [Makefile]
 indent_style = tab
+
+[*.go]
+indent_style = tab

.gitea/workflows/release.yml

@@ -16,11 +16,12 @@ jobs:
           fetch-depth: 0
       # goreleaser is not a compiler: it shells out to `go` for the
       # `before:` hook and for every one of the four cross-compiles.
-      # Nothing else in this repo puts a Go toolchain on the runner --
-      # check.yml runs script/cibuild, which does all of its work inside
-      # the digest-pinned Dockerfile images -- so without this step the
-      # release either fails at the before-hook or, worse, ships binaries
-      # built by whatever Go the runner happens to carry.
+      # Without this step the release either fails at the before-hook or,
+      # worse, ships binaries built by whatever Go the runner happens to
+      # carry. check.yml's script/cibuild also puts Go on its own runner,
+      # through script/bootstrap from the package manager at whatever
+      # version that ships, but uses it only for `go mod download` and
+      # gofmt; it compiles inside the digest-pinned Dockerfile images.
       #
       # actions/setup-go would pin the action by commit sha, but the Go
       # tarball it downloads at runtime is verified against no value in

.gitignore

@@ -45,3 +45,18 @@ node_modules/
 [iI][dD]_[eE][cC][dD][sS][aA]_[sS][kK]
 [iI][dD]_[eE][dD]25519
 [iI][dD]_[eE][dD]25519_[sS][kK]
+
+# Go build and test output.
+*.log
+*.out
+*.test
+coverage.html
+
+# This repo's own host-built artifacts.
+/vaultik
+/dist/
+/.tool/
+
+# Local configs for development; they hold storage credentials.
+local-config.yaml
+dev-config.yaml

AGENTS.md

@@ -128,4 +128,3 @@ Version: 2025-06-08
 
 18. For estimates: backing up over 2.5Gbit/s ethernet to an S3 server
     backed by 2000MB/sec SSD takes about 4 seconds per gigabyte.
-

ARCHITECTURE.md

@@ -353,7 +353,7 @@ CreateSnapshot(opts)
 
 ## Deduplication Strategy
 
-1. **File-level**: Files unchanged since last backup are skipped (metadata comparison: size, mtime, mode, uid, gid)
+1. **File-level**: Files unchanged since last backup are skipped (metadata comparison: size, mtime, mode, uid, gid), unless the file lists a chunk that no uploaded blob holds; such a file is re-chunked
 
 2. **Chunk-level**: Chunks are content-addressed by SHA256 hash. If a chunk hash already exists in the database, the chunk data is not re-uploaded.
 

Dockerfile

@@ -43,9 +43,10 @@ COPY . .
 # `git describe --tags --always` on the .git in the build context. With
 # .git present, a version that is still empty, dev or unknown fails the
 # build: git is missing or could not read the checkout. The commit and
-# its date always come from that .git, and are "unknown" without one.
+# its date always come from that .git. A context without .git, such as
+# a source export, stamps "dev" and an "unknown" commit and date.
 ARG VERSION
-RUN VERSION="${VERSION:-$(git describe --tags --always)}"; \
+RUN VERSION="${VERSION:-$(git describe --tags --always || echo dev)}"; \
     if [ -e .git ]; then \
         case "$VERSION" in ""|dev|unknown) \
             echo "version is '$VERSION' although .git is present" >&2; \

README.md

@@ -40,7 +40,8 @@ Features:
 
 * modern encryption ([age](https://age-encryption.org/), X25519 + ChaCha20-Poly1305)
 * content-defined chunking with deduplication (FastCDC)
-* incremental backups (only changed files are re-chunked)
+* incremental backups (a file is re-chunked only when it changed or a
+  chunk it lists is held by no uploaded blob)
 * multithreaded zstd compression at configurable levels
 * content-addressed immutable storage
 * local state tracking in SQLite (enables write-only incremental backups)
@@ -499,8 +500,9 @@ format does and does not protect.
 
 * Content-defined chunking using the FastCDC algorithm
 * Average chunk size: configurable (default 10MB)
-* Deduplication at file level (unchanged files skipped) and chunk level
-  (identical chunks across files stored once)
+* Deduplication at file level (unchanged files skipped, unless a chunk
+  the file lists is held by no uploaded blob) and chunk level (identical
+  chunks across files stored once)
 * Multiple chunks packed into blobs to reduce object count
 
 ### encryption

TODO.md

@@ -31,6 +31,15 @@ the tag exists and is exercised; what is left is merging `next` to
   is v2.14.0, with its new findings fixed in the code, and the rules in
   `CLAUDE.md` now live in `AGENTS.md`.
 
+- 2026-10-06: Made a backup re-chunk a known file that lists a chunk no
+  uploaded blob holds
+  ([issue #214](https://git.eeqj.de/sneak/vaultik/issues/214)). File
+  rows are shared by every snapshot and updated in place, so removing or
+  pruning the only snapshot that referenced a changed file's current
+  blob left an older snapshot keeping a row that matched the disk while
+  no blob held its chunks. The next backup skipped the file and
+  completed a snapshot that could not restore it.
+
 - 2026-09-22: Routed the last direct-to-stdout command output through
   `internal/ui`
   ([issue #149](https://git.eeqj.de/sneak/vaultik/issues/149)). The

cmd/vaultik/dockerversion_test.go

@@ -45,9 +45,9 @@ func TestProductDockerfileTakesVersionAsBuildArg(t *testing.T) {
 
 // TestProductDockerfileDerivesVersionFromGit fails unless a build given
 // no VERSION, such as a plain `docker build .` of a clone, takes it from
-// `git describe` of the .git in its context, and fails rather than
-// stamp "dev" when that .git yields no version. The commit and its date
-// come from the same .git.
+// `git describe` of the .git in its context, stamps "dev" when the
+// context has no .git, and fails rather than stamp "dev" when that .git
+// yields no version. The commit and its date come from the same .git.
 func TestProductDockerfileDerivesVersionFromGit(t *testing.T) {
 	t.Parallel()
 
@@ -56,9 +56,9 @@ func TestProductDockerfileDerivesVersionFromGit(t *testing.T) {
 	buildAt := indexContaining(found, "go build")
 	require.GreaterOrEqual(t, buildAt, 0, "%s must build", productDockerfile)
 
-	assert.Contains(t, found[buildAt], "git describe --tags --always",
-		"%s must derive the version from git when no VERSION is given",
-		productDockerfile)
+	assert.Contains(t, found[buildAt], "git describe --tags --always || echo dev",
+		"%s must derive the version from git when no VERSION is given,"+
+			" and stamp dev when the context has no .git", productDockerfile)
 	assert.Contains(t, found[buildAt], "[ -e .git ]",
 		"%s must fail when the context carries .git but yields no version",
 		productDockerfile)

docs/DATAMODEL.md

@@ -195,6 +195,7 @@ Tracks blob upload metrics.
 1. **Change Detection**
    - `SELECT * FROM files WHERE path = ?` - Get previous file metadata
    - Compare mtime, size, mode to detect changes
+   - Re-chunk a file that lists a chunk no uploaded blob holds, even when its metadata is unchanged
    - Skip unchanged files but still add to `snapshot_files`
 
 2. **Chunk Reuse**

internal/database/files.go

@@ -266,6 +266,56 @@ func (r *FileRepository) ListByPrefix(
 	return files, rows.Err()
 }
 
+// ListIDsWithChunksNotInUploadedBlobs returns the IDs of the files whose
+// path starts with prefix and that list at least one chunk held by no
+// blob whose upload has completed (uploaded_ts set). A new snapshot
+// cannot reference such a chunk, so a backup must not treat the file as
+// unchanged even when its metadata matches the file on disk.
+func (r *FileRepository) ListIDsWithChunksNotInUploadedBlobs(
+	ctx context.Context, prefix string,
+) ([]types.FileID, error) {
+	query := `
+		SELECT DISTINCT f.id
+		FROM files f
+		JOIN file_chunks fc ON fc.file_id = f.id
+		WHERE f.path LIKE ? || '%'
+		  AND NOT EXISTS (
+			SELECT 1
+			FROM blob_chunks bc
+			JOIN blobs b ON bc.blob_id = b.id
+			WHERE bc.chunk_hash = fc.chunk_hash
+			  AND b.uploaded_ts IS NOT NULL
+		  )
+	`
+
+	rows, err := r.db.conn.QueryContext(ctx, query, prefix)
+	if err != nil {
+		return nil, fmt.Errorf("querying files: %w", err)
+	}
+
+	defer func() {
+		err := rows.Close()
+		if err != nil {
+			Fatalf("failed to close rows: %v", err)
+		}
+	}()
+
+	var ids []types.FileID
+
+	for rows.Next() {
+		var id types.FileID
+
+		err := rows.Scan(&id)
+		if err != nil {
+			return nil, fmt.Errorf("scanning file ID: %w", err)
+		}
+
+		ids = append(ids, id)
+	}
+
+	return ids, rows.Err()
+}
+
 // ListAll returns all files in the database
 func (r *FileRepository) ListAll(ctx context.Context) ([]*File, error) {
 	query := `

internal/snapshot/scanner.go

@@ -73,6 +73,11 @@ type Scanner struct {
 	knownChunks   map[string]struct{}
 	knownChunksMu sync.RWMutex
 
+	// filesToRechunk holds the IDs of known files that list a chunk no
+	// uploaded blob holds; they are re-chunked even when their metadata
+	// is unchanged.
+	filesToRechunk map[types.FileID]struct{}
+
 	// Pending chunk hashes - chunks that have been added to packer but not
 	// yet committed to DB. When a blob finalizes, the committed chunks are
 	// removed from this set.
@@ -325,9 +330,42 @@ func (s *Scanner) loadDatabaseState(
 	s.ui.Completef("Loaded %s known chunks from local index database.",
 		s.ui.Count(len(s.knownChunks)))
 
+	err = s.loadFilesToRechunk(ctx, path)
+	if err != nil {
+		return nil, fmt.Errorf("loading files to re-chunk: %w", err)
+	}
+
 	return knownFiles, nil
 }
 
+// loadFilesToRechunk loads the IDs of known files under path that list a
+// chunk no uploaded blob holds. A file row is shared by every snapshot
+// that lists the file and is updated in place when the file changes,
+// while a blob row is deleted once no snapshot references it. Removing
+// the only snapshot that references a changed file's current blob
+// therefore leaves an older snapshot keeping a file row whose metadata
+// matches the disk while no blob the local index records as uploaded
+// holds its chunks, so a new snapshot cannot reference them. The dropped
+// blob can still be in remote storage until prune removes it.
+func (s *Scanner) loadFilesToRechunk(ctx context.Context, path string) error {
+	ids, err := s.repos.Files.ListIDsWithChunksNotInUploadedBlobs(ctx, path)
+	if err != nil {
+		return fmt.Errorf("listing files: %w", err)
+	}
+
+	s.filesToRechunk = make(map[types.FileID]struct{}, len(ids))
+	for _, id := range ids {
+		s.filesToRechunk[id] = struct{}{}
+	}
+
+	if len(ids) > 0 {
+		log.Info("Re-chunking known files whose chunks are not all "+
+			"in uploaded blobs", "files", len(ids))
+	}
+
+	return nil
+}
+
 // repairInterruptedBlobs discards blob rows left by a previous run whose
 // upload never completed. Such a blob has its chunks, blob_chunks, and
 // blobs rows committed to the local index before the upload is attempted,
@@ -1208,6 +1246,11 @@ func (s *Scanner) checkFileInMemory(
 		return file, true
 	}
 
+	// No uploaded blob holds one of its chunks (see loadFilesToRechunk)
+	if _, rechunk := s.filesToRechunk[fileID]; rechunk {
+		return file, true
+	}
+
 	// Check if file has changed
 	if existingFile.Size != file.Size ||
 		existingFile.MTime.Unix() != file.MTime.Unix() ||

internal/vaultik/changed_file_restore_test.go

@@ -0,0 +1,234 @@
+package vaultik_test
+
+import (
+	"context"
+	"crypto/rand"
+	"path/filepath"
+	"slices"
+	"strings"
+	"testing"
+
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/require"
+	"sneak.berlin/go/vaultik/internal/chunker"
+	"sneak.berlin/go/vaultik/internal/config"
+	"sneak.berlin/go/vaultik/internal/database"
+	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/storage"
+	"sneak.berlin/go/vaultik/internal/storage/faultstore"
+	"sneak.berlin/go/vaultik/internal/vaultik"
+)
+
+// These tests cover https://git.eeqj.de/sneak/vaultik/issues/214: once
+// the only snapshot referencing a changed file's current blob is
+// dropped, an older snapshot still keeps the file's row, and the next
+// backup must re-chunk the file instead of treating it as unchanged.
+//
+// Each backup run uses its own snapshot name over the same source
+// directory, so the snapshot IDs differ without waiting for their
+// one-second timestamps to tick over. File rows are keyed by path, so
+// the runs share them exactly as runs of one snapshot name would.
+
+// changedFileConfig returns a full-backup config with the snapshot names
+// "first", "second" and "third", all backing up dataDir.
+func changedFileConfig(dataDir, dbPath string) *config.Config {
+	source := config.SnapshotConfig{Paths: []string{dataDir}}
+
+	cfg := faultTestConfig()
+	cfg.IndexPath = dbPath
+	cfg.ChunkSize = config.Size(faultChunkSize)
+	cfg.Snapshots = map[string]config.SnapshotConfig{
+		"first":  source,
+		"second": source,
+		"third":  source,
+	}
+
+	return cfg
+}
+
+// backUp runs a full backup of the named snapshot.
+func backUp(v *vaultik.Vaultik, name string) error {
+	return v.CreateSnapshot(&vaultik.SnapshotCreateOptions{
+		Cron:      true,
+		Snapshots: []string{name},
+	})
+}
+
+// appendedFileSize is the size of the file before the tests append to it.
+// It is twice the largest chunk the chunker cuts, so the file's first
+// chunk ends before the appended bytes and stays in a blob the first
+// snapshot still references, while its new chunks are only in the blob
+// that gets dropped.
+const appendedFileSize = 2 * chunker.ChunkSizeSpread * faultChunkSize
+
+// appendRandomBytes appends n random bytes to the file at path, creating
+// the file if it does not exist, and records the new content in files.
+// Random content gives the chunker real cut points.
+func appendRandomBytes(
+	t *testing.T, fs afero.Fs, files map[string][]byte, path string, n int64,
+) {
+	t.Helper()
+
+	added := make([]byte, n)
+	_, err := rand.Read(added)
+	require.NoError(t, err)
+
+	content := slices.Concat(files[path], added)
+	require.NoError(t, afero.WriteFile(fs, path, content, 0o644))
+
+	files[path] = content
+}
+
+// localSnapshotID returns the ID of the one snapshot in the local index
+// that was backed up under name.
+func localSnapshotID(
+	ctx context.Context, t *testing.T,
+	repos *database.Repositories, name string,
+) string {
+	t.Helper()
+
+	snapshots, err := repos.Snapshots.ListRecent(ctx, listRecentTestLimit)
+	require.NoError(t, err)
+
+	var ids []string
+
+	for _, s := range snapshots {
+		if strings.Contains(s.ID.String(), "_"+name+"_") {
+			ids = append(ids, s.ID.String())
+		}
+	}
+
+	require.Lenf(t, ids, 1, "expected one local snapshot named %q", name)
+
+	return ids[0]
+}
+
+// assertThirdSnapshotRestores closes the local index, then restores the
+// snapshot named "third" from store alone and byte-compares every file
+// against files.
+func assertThirdSnapshotRestores(
+	ctx context.Context, t *testing.T, cfg *config.Config,
+	store storage.Storer, repos *database.Repositories, db *database.DB,
+	fs afero.Fs, restoreDir string, files map[string][]byte,
+) {
+	t.Helper()
+
+	id := localSnapshotID(ctx, t, repos, "third")
+	require.NoError(t, db.Close())
+
+	reader := newReaderVaultik(ctx, cfg, store, nil, fs)
+	require.NoError(t, reader.Restore(&vaultik.RestoreOptions{
+		SnapshotID: id,
+		TargetDir:  restoreDir,
+		Verify:     true,
+	}), "the backup after the drop must restore the changed file")
+
+	assertRestoredTree(t, fs, restoreDir, files)
+}
+
+// Trigger 1: bytes are appended to the file, a second snapshot backs it
+// up, and that snapshot is removed. The first snapshot keeps the file row,
+// which now lists the appended content's chunks, while removal drops the
+// blob that held them.
+//
+//nolint:paralleltest // installs the global logger via log.Initialize
+func TestBackupAfterRemovingNewestSnapshotRestoresChangedFile(t *testing.T) {
+	log.Initialize(log.Config{})
+
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+	dataDir := filepath.Join(tempDir, "src")
+	storeDir := filepath.Join(tempDir, "remote")
+	restoreDir := filepath.Join(tempDir, "restored")
+	dbPath := filepath.Join(tempDir, "index.sqlite")
+	changedPath := filepath.Join(dataDir, "appended.bin")
+
+	ctx := context.Background()
+	files := writeFaultSourceTree(t, fs, dataDir)
+	cfg := changedFileConfig(dataDir, dbPath)
+
+	appendRandomBytes(t, fs, files, changedPath, appendedFileSize)
+
+	store, err := storage.NewFileStorer(storeDir)
+	require.NoError(t, err)
+
+	db, err := database.New(ctx, dbPath)
+	require.NoError(t, err)
+
+	repos := database.NewRepositories(db)
+	v := newBackupVaultik(ctx, cfg, store, repos, db, fs)
+
+	require.NoError(t, backUp(v, "first"))
+
+	appendRandomBytes(t, fs, files, changedPath, faultChunkSize)
+	require.NoError(t, backUp(v, "second"))
+
+	_, err = v.RemoveSnapshot(localSnapshotID(ctx, t, repos, "second"),
+		&vaultik.RemoveOptions{Force: true})
+	require.NoError(t, err)
+
+	require.NoError(t, backUp(v, "third"))
+
+	assertThirdSnapshotRestores(
+		ctx, t, cfg, store, repos, db, fs, restoreDir, files)
+}
+
+// Trigger 2: bytes are appended to the file and the run that backs it up
+// is interrupted at the manifest upload, after its blobs were uploaded.
+// The next run's prune drops that incomplete snapshot and its blob, while
+// the first snapshot keeps the file row, which now lists the appended
+// content's chunks.
+//
+//nolint:paralleltest // installs the global logger via log.Initialize
+func TestBackupAfterInterruptedRunRestoresChangedFile(t *testing.T) {
+	log.Initialize(log.Config{})
+
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+	dataDir := filepath.Join(tempDir, "src")
+	storeDir := filepath.Join(tempDir, "remote")
+	restoreDir := filepath.Join(tempDir, "restored")
+	dbPath := filepath.Join(tempDir, "index.sqlite")
+	changedPath := filepath.Join(dataDir, "appended.bin")
+
+	ctx := context.Background()
+	files := writeFaultSourceTree(t, fs, dataDir)
+	cfg := changedFileConfig(dataDir, dbPath)
+
+	appendRandomBytes(t, fs, files, changedPath, appendedFileSize)
+
+	inner, err := storage.NewFileStorer(storeDir)
+	require.NoError(t, err)
+
+	failManifest := false
+	store := faultstore.New(inner)
+	store.OnPut = func(key string) faultstore.PutAction {
+		if failManifest && strings.HasSuffix(key, "manifest.json.zst") {
+			return faultstore.PutFail
+		}
+
+		return faultstore.PutNormal
+	}
+
+	db, err := database.New(ctx, dbPath)
+	require.NoError(t, err)
+
+	repos := database.NewRepositories(db)
+	v := newBackupVaultik(ctx, cfg, store, repos, db, fs)
+
+	require.NoError(t, backUp(v, "first"))
+
+	appendRandomBytes(t, fs, files, changedPath, faultChunkSize)
+
+	failManifest = true
+
+	require.Error(t, backUp(v, "second"),
+		"the run must fail when its manifest upload fails")
+
+	failManifest = false
+
+	require.NoError(t, backUp(v, "third"))
+
+	assertThirdSnapshotRestores(
+		ctx, t, cfg, inner, repos, db, fs, restoreDir, files)
+}

script/install-go

@@ -7,10 +7,11 @@
 # Only .gitea/workflows/release.yml calls this. goreleaser is not a
 # compiler: it shells out to `go` for the `before:` hook and for every
 # one of the four cross-compiles, so the release runner needs a Go
-# toolchain on PATH. check.yml compiles nothing on the host: its one
-# host use of Go is gofmt in script/fmt-check, with whatever Go
-# script/bootstrap finds or installs. So this is the release path's only
-# host Go, and per REPO_POLICIES.md it must be pinned by hash.
+# toolchain on PATH. check.yml compiles nothing on the host: it uses
+# whatever Go script/bootstrap finds or installs only for that script's
+# `go mod download` and for gofmt in script/fmt-check. So this is the
+# only host Go that builds anything, and per REPO_POLICIES.md it must be
+# pinned by hash.
 # actions/setup-go exposes no checksum input, so Go is installed the way
 # script/install-goreleaser installs goreleaser: download the exact
 # archive from go.dev and refuse it unless its sha256 matches the value