Reconcile docs with code across the accuracy-sweep items (closes #74)

Documentation only. Corrects the ARCHITECTURE.md chunk sizes and the fx
config type; documents the process-wide PID lock, the `ls`/`rm` aliases,
`VAULTIK_CPUPROFILE`/`VAULTIK_MEMPROFILE`, the `age_secret_key` key and
its threat-model caveat, and how zstd levels 1-19 collapse onto four
presets; narrows the output-style claim to match reality; and links
ARCHITECTURE.md and config.example.yml from the README. The two
behaviour changes the sweep surfaced are deferred to #149 (route direct
stdout through internal/ui) and #150 (scope the lock), each linked from
the text. DATAMODEL.md and REPOSTRUCTURE.md were already linked.

model: claude-opus-4-8

ARCHITECTURE.md

@@ -63,7 +63,7 @@ A content-addressed unit of data. Files are split into variable-size chunks usin
 - `ChunkHash`: SHA256 hash of chunk content (primary key)
 - `Size`: Chunk size in bytes
 
-Chunk sizes vary between `avgChunkSize/4` and `avgChunkSize*4` (typically 16KB-256KB for 64KB average).
+Chunk sizes vary between `avgChunkSize/4` and `avgChunkSize*4` (2.5MB-40MB for the 10MB default average).
 
 #### FileChunk (`database.FileChunk`)
 Maps files to their constituent chunks:
@@ -120,7 +120,7 @@ The CLI uses fx for dependency injection. Here's the instantiation order:
 ```go
 // cli/app.go: NewApp()
 fx.New(
-    fx.Supply(config.ConfigPath(opts.ConfigPath)),  // 1. Config path
+    fx.Supply(config.Path(opts.ConfigPath)),         // 1. Config path
     fx.Supply(opts.LogOptions),                      // 2. Log options
     fx.Provide(globals.New),                         // 3. Globals
     fx.Provide(log.New),                             // 4. Logger config
@@ -193,7 +193,7 @@ scanner := v.ScannerFactory(snapshot.ScannerParams{
 - **Created by**: `chunker.NewChunker(avgChunkSize)`
 - **When**: Inside `snapshot.NewScanner()`
 - **Configuration**:
-  - `avgChunkSize`: From config (typically 64KB)
+  - `avgChunkSize`: From config (default 10MB)
   - `minChunkSize`: avgChunkSize / 4
   - `maxChunkSize`: avgChunkSize * 4
 

README.md

@@ -147,10 +147,10 @@ vaultik [--config <path>] config edit
 vaultik [--config <path>] config get <key>
 vaultik [--config <path>] config set <key> <value>
 vaultik [--config <path>] snapshot create [snapshot-names...] [--cron] [--prune] [--keep-newer-than <duration>]
-vaultik [--config <path>] snapshot list [--json]
+vaultik [--config <path>] snapshot list [--json]                  # alias: ls
 vaultik [--config <path>] snapshot verify <snapshot-id> [--deep] [--json]
 vaultik [--config <path>] snapshot purge [--keep-latest | --older-than <duration>] [--snapshot <name>...] [--force]
-vaultik [--config <path>] snapshot remove <snapshot-id> [--dry-run] [--force] [--local-only] [--json]
+vaultik [--config <path>] snapshot remove <snapshot-id> [--dry-run] [--force] [--local-only] [--json]  # alias: rm
 vaultik [--config <path>] snapshot restore <snapshot-id> <target-dir> [paths...] [--verify]
 vaultik [--config <path>] prune [--force] [--json]
 vaultik [--config <path>] info
@@ -169,6 +169,21 @@ vaultik version
 * `--quiet`, `-q`: Suppress non-error output (also suppresses startup banner)
 * `--skip-errors`: Continue past per-file errors instead of aborting (applies to `snapshot create` and `restore`)
 
+### locking
+
+Every command that opens the local index — `snapshot create`, `snapshot
+list`, `snapshot verify`, `snapshot purge`, `snapshot remove`, `snapshot
+restore`, `prune`, `info`, and `remote info`/`remote nuke` — takes a
+process-wide lock at `$XDG_DATA_HOME/vaultik/vaultik.pid`
+(`~/.local/share/vaultik/vaultik.pid` on Linux) for the whole run. Only
+one such command runs at a time: a second one exits immediately with an
+"already running" error rather than waiting. The lock is not scoped to
+mutating commands, so read-only commands are affected too — `vaultik
+snapshot list` fails while a backup is in progress; scoping it so
+read-only commands run during a backup is tracked in
+[issue #150](https://git.eeqj.de/sneak/vaultik/issues/150). `config`,
+`database delete`, `completion`, and `version` do not take the lock.
+
 ### stdout and stderr
 
 Log output — everything from `--verbose` and `--debug`, and every
@@ -203,6 +218,8 @@ and `vaultik prune --json | jq .` both work as written.
 * `VAULTIK_AGE_SECRET_KEY`: Age private key for decryption (required for `snapshot restore` and `snapshot verify --deep`)
 * `VAULTIK_CONFIG`: Path to config file (overridden by `--config`)
 * `VAULTIK_INDEX_PATH`: Override local SQLite index path
+* `VAULTIK_CPUPROFILE`: Write a CPU profile to this path for the duration of the run (development/debugging)
+* `VAULTIK_MEMPROFILE`: Write a heap profile to this path when the run exits (development/debugging)
 
 ### shell completion
 
@@ -395,6 +412,10 @@ both are set.
 
 ## architecture
 
+For an implementation-level view of the internals — the data model, the
+`fx` dependency-injection wiring, and the scanner — see
+[`ARCHITECTURE.md`](ARCHITECTURE.md).
+
 ### remote storage layout
 
 ```
@@ -472,19 +493,24 @@ derivation.
 
 ### compression
 
-* zstd compression at configurable level (1-19, default 3)
+* zstd compression at configurable level (1-19, default 3). The level is
+  accepted as 1-19 but maps onto zstd's four internal speed presets:
+  1-2 fastest, 3-5 default, 6-9 better, 10-19 best. Levels within the
+  same band compress identically.
 * Applied before encryption at the blob level
 
 ---
 
 ## configuration reference
 
-Run `vaultik config init` to generate a fully commented config file.
+Run `vaultik config init` to generate a fully commented config file; a
-Key fields:
+complete annotated example also lives in
+[`config.example.yml`](config.example.yml). Key fields:
 
 | Field | Default | Description |
 |-------|---------|-------------|
 | `age_recipients` | (required) | Age public keys for encryption |
+| `age_secret_key` | (unset) | Age private key for decryption (`snapshot restore`, `snapshot verify --deep`). Setting it in the config file places the private key on the backed-up host, defeating the public-key-only design (see "why" above). Prefer the `VAULTIK_AGE_SECRET_KEY` environment variable, supplied only on the machine you restore from. |
 | `snapshots` | (required) | Named snapshot definitions with paths and excludes |
 | `storage_url` | | Storage backend URL (`s3://`, `file://`, `rclone://`) |
 | `s3.*` | | Legacy S3 configuration (endpoint, bucket, credentials) |
@@ -600,9 +626,17 @@ priority.
 
 ## output style
 
-All user-facing output goes through helpers in `internal/ui` and conforms
+The operational narration of the long-running commands — the Begin,
-to a uniform style. Color is enabled when stdout is a TTY and the
+Complete, Progress, and status lines of `snapshot create`, `prune`,
-`NO_COLOR` environment variable is unset (https://no-color.org/).
+`snapshot restore`, and the like — goes through helpers in `internal/ui`
+and conforms to the uniform style below. Some commands instead write
+plain text straight to stdout (`version`, `info`, `config`, the
+`database delete` prompt, and the `snapshot list` table); that output is
+unstyled and does not honor `--quiet`. Routing it through `internal/ui`
+is tracked in
+[issue #149](https://git.eeqj.de/sneak/vaultik/issues/149). Color is
+enabled when stdout is a TTY and the `NO_COLOR` environment variable is
+unset (https://no-color.org/).
 
 `internal/ui` writes to stdout; it is the output the user asked for.
 Structured log records are a different thing and go through

TODO.md

@@ -25,17 +25,6 @@ release" is exactly the contradiction
 
 # Completed Steps
 
-- 2026-09-21: Stopped `--json` from silencing stderr diagnostics
-  ([issue #112](https://git.eeqj.de/sneak/vaultik/issues/112)). `--json`
-  used to be folded into `Quiet`, which pinned the log level to `WARN`,
-  so `prune --json` gave a machine consumer no record of the local index
-  rows it deleted even under `--verbose`. `--json` now quiets only the
-  stdout UI (the JSON document must stay clean, per
-  [issue #108](https://git.eeqj.de/sneak/vaultik/issues/108)); the stderr
-  log level follows `--verbose`/`--debug` again. The coupling was
-  removed the same way for `snapshot verify`, `snapshot remove`, and
-  `remote info`, which carried it for the same outdated reason.
-
 - 2026-09-21: Stopped `prune` from reporting a failed row count as 0
   ([issue #96](https://git.eeqj.de/sneak/vaultik/issues/96)). The seven
   `getTableCount` reads in `PruneDatabase` discarded their error, so a

internal/cli/app.go

@@ -49,11 +49,6 @@ type AppOptions struct {
 // silenced — per the documented convention that --quiet suppresses
 // non-error output only. The startup banner is printed by Entry
 // before cobra parses arguments, gated by the same arg-level check.
-//
-// --json quiets the UI here too, because stdout then carries a JSON
-// document and human narration would corrupt it. Unlike Quiet it does
-// not lower the stderr log level (issue #112), so --verbose/--debug
-// still surface diagnostics alongside the document.
 func setupGlobals(
 	lc fx.Lifecycle, g *globals.Globals, v *vaultik.Vaultik, opts log.Options,
 ) {
@@ -61,7 +56,7 @@ func setupGlobals(
 		OnStart: func(_ context.Context) error {
 			g.StartTime = time.Now().UTC()
 
-			if opts.Cron || opts.Quiet || opts.JSON {
+			if opts.Cron || opts.Quiet {
 				v.UI.SetQuiet(true)
 			}
 
@@ -284,11 +279,10 @@ func RunOperation(
 // shared by the list/purge/verify/remove/remote-info subcommands:
 // resolve the config, then run op against the Vaultik instance through
 // RunOperation, reporting a failure prefixed with failMsg (suppressed
-// while suppressErrors is true, e.g. under --json). jsonOutput marks a
+// while suppressErrors is true, e.g. under --json). extraQuiet is OR-ed
-// command whose stdout is a JSON document: it quiets the UI but, unlike
+// into LogOptions.Quiet (e.g. --json output modes).
-// Quiet, leaves the stderr log level alone.
 func runVaultikApp(
-	cmd *cobra.Command, jsonOutput, suppressErrors bool,
+	cmd *cobra.Command, extraQuiet, suppressErrors bool,
 	failMsg string, op func(v *vaultik.Vaultik) error,
 ) error {
 	configPath, err := ResolveConfigPath()
@@ -303,8 +297,7 @@ func runVaultikApp(
 		LogOptions: log.Options{
 			Verbose: rootFlags.Verbose,
 			Debug:   rootFlags.Debug,
-			Quiet:   rootFlags.Quiet,
+			Quiet:   rootFlags.Quiet || extraQuiet,
-			JSON:    jsonOutput,
 		},
 	}, op, func(err error) {
 		if suppressErrors {

internal/cli/entry_prune_json_stderr_test.go

@@ -1,140 +0,0 @@
-package cli //nolint:testpackage // shares the prune fixtures and capture helpers
-
-import (
-	"bytes"
-	"io"
-	"os"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// staleRecordLogMessage is the local-cleanup audit line CleanupLocalSnapshots
-// logs for each stale record. It is exactly the signal issue #112 says a
-// machine consumer lost under --json: gated off stdout, and pinned below
-// the log level on stderr because --json used to force Quiet.
-const staleRecordLogMessage = "Removing stale local snapshot record"
-
-// TestEntryPruneJSONStderrHonoursVerbosity is the end-to-end regression
-// guard for issue #112. Under --json the log level must still follow
-// --verbose/--debug rather than being pinned to WARN, so the
-// local-cleanup records reach stderr under --verbose while stdout stays
-// exactly one JSON document; without --verbose they stay below the
-// level, as they do without --json.
-//
-// Both halves are asserted together on the same run, because the fix has
-// to keep the document clean (issue #108) while freeing stderr.
-//
-// Not parallel: it replaces os.Args, os.Stdout, os.Stderr and the xdg
-// globals.
-//
-//nolint:paralleltest // replaces os.Args, os.Stdout, os.Stderr and the xdg globals
-func TestEntryPruneJSONStderrHonoursVerbosity(t *testing.T) {
-	for _, testCase := range []struct {
-		name         string
-		verbose      bool
-		wantOnStderr bool
-	}{
-		{
-			name:         "verbose json surfaces the cleanup record on stderr",
-			verbose:      true,
-			wantOnStderr: true,
-		},
-		{
-			name:         "json alone keeps the cleanup record below the level",
-			verbose:      false,
-			wantOnStderr: false,
-		},
-	} {
-		t.Run(testCase.name, func(t *testing.T) {
-			configPath := writeHermeticPruneConfig(t, true)
-
-			previousArgs := os.Args
-
-			t.Cleanup(func() {
-				os.Args = previousArgs
-				rootFlags = RootFlags{}
-			})
-
-			args := []string{
-				programName, flagConfig, configPath, cmdPrune, flagJSON,
-			}
-			if testCase.verbose {
-				args = append(args, "--verbose")
-			}
-
-			os.Args = args
-
-			stdout, stderr := captureProcessStdoutAndStderr(t,
-				func() { _ = Entry() })
-
-			// The document stays clean in both cases: freeing stderr must
-			// not regress issue #108.
-			requireExactlyOneJSONDocument(t, stdout)
-
-			if testCase.wantOnStderr {
-				assert.Contains(t, stderr, staleRecordLogMessage,
-					"--verbose --json must emit the cleanup record on stderr")
-				assert.Contains(t, stderr, stalePruneSnapshotID,
-					"the record must name the snapshot it removed")
-			} else {
-				assert.NotContains(t, stderr, staleRecordLogMessage,
-					"without --verbose the record stays below the log level")
-			}
-		})
-	}
-}
-
-// captureProcessStdoutAndStderr redirects both of the process's own
-// standard streams to pipes for the duration of fn and returns what was
-// written to each. The redirection is at the file-descriptor level
-// because the logger binds os.Stderr when it initializes inside fn, and
-// the JSON document reaches os.Stdout independently; the point is to see
-// where each actually lands.
-//
-// Not parallel-safe: os.Stdout and os.Stderr are process-global.
-func captureProcessStdoutAndStderr(t *testing.T, fn func()) (string, string) {
-	t.Helper()
-
-	outReader, outWriter, err := os.Pipe()
-	require.NoError(t, err)
-
-	errReader, errWriter, err := os.Pipe()
-	require.NoError(t, err)
-
-	previousOut, previousErr := os.Stdout, os.Stderr
-	os.Stdout, os.Stderr = outWriter, errWriter
-
-	capturedOut := drain(outReader)
-	capturedErr := drain(errReader)
-
-	fn()
-
-	os.Stdout, os.Stderr = previousOut, previousErr
-
-	require.NoError(t, outWriter.Close())
-	require.NoError(t, errWriter.Close())
-
-	out, errOut := <-capturedOut, <-capturedErr
-
-	require.NoError(t, outReader.Close())
-	require.NoError(t, errReader.Close())
-
-	return out, errOut
-}
-
-// drain copies a reader to a string on a goroutine and delivers the
-// result once the writer end is closed.
-func drain(reader io.Reader) <-chan string {
-	captured := make(chan string, 1)
-
-	go func() {
-		var buf bytes.Buffer
-
-		_, _ = io.Copy(&buf, reader)
-		captured <- buf.String()
-	}()
-
-	return captured
-}

internal/cli/prune.go

@@ -41,8 +41,7 @@ work (e.g. after a crashed backup or to reclaim storage).`,
 				LogOptions: log.Options{
 					Verbose: rootFlags.Verbose,
 					Debug:   rootFlags.Debug,
-					Quiet:   rootFlags.Quiet,
+					Quiet:   rootFlags.Quiet || opts.JSON,
-					JSON:    opts.JSON,
 				},
 			}, func(v *vaultik.Vaultik) error {
 				return v.Prune(opts)

internal/cli/remote.go

@@ -85,8 +85,7 @@ func newRemoteInfoCommand() *cobra.Command {
 				LogOptions: log.Options{
 					Verbose: rootFlags.Verbose,
 					Debug:   rootFlags.Debug,
-					Quiet:   rootFlags.Quiet,
+					Quiet:   rootFlags.Quiet || jsonOutput,
-					JSON:    jsonOutput,
 				},
 			}, func(v *vaultik.Vaultik) error {
 				return v.RemoteInfo(jsonOutput)

internal/cli/snapshot.go

@@ -209,8 +209,7 @@ func newSnapshotVerifyCommand() *cobra.Command {
 				LogOptions: log.Options{
 					Verbose: rootFlags.Verbose,
 					Debug:   rootFlags.Debug,
-					Quiet:   rootFlags.Quiet,
+					Quiet:   rootFlags.Quiet || opts.JSON,
-					JSON:    opts.JSON,
 				},
 			}, func(v *vaultik.Vaultik) error {
 				return v.VerifySnapshotWithOptions(snapshotID, opts)

internal/log/module.go

@@ -14,18 +14,8 @@ var Module = fx.Module("log",
 )
 
 // New creates a new logger configuration from provided options.
-//
-// JSON is intentionally not carried into Config: a command emitting a
-// JSON document on stdout must keep its stderr log level under
-// --verbose/--debug, so --json must not lower it (issue #112). JSON
-// silences the stdout UI in setupGlobals instead.
 func New(opts Options) Config {
-	return Config{
+	return Config(opts)
-		Verbose: opts.Verbose,
-		Debug:   opts.Debug,
-		Cron:    opts.Cron,
-		Quiet:   opts.Quiet,
-	}
 }
 
 // Options are provided by the CLI.
@@ -34,8 +24,4 @@ type Options struct {
 	Debug   bool
 	Cron    bool
 	Quiet   bool
-	// JSON marks a command whose stdout carries a machine-readable
-	// document. It silences the human UI on stdout (see setupGlobals),
-	// but unlike Quiet it leaves the stderr log level alone.
-	JSON bool
 }