Exclude dotfiles by default, add --include-dotfiles flag

Changed the default behavior to exclude dotfiles (files/dirs starting with .)
which is the more common use case. Added --include-dotfiles flag for when
hidden files need to be included in the manifest.

Makefile

@@ -19,7 +19,7 @@ default: fmt test
 
 run: ./mfer.cmd
 	./$<
-	./$< gen --ignore-dotfiles
+	./$< gen
 
 ci: test
 

README.md

@@ -101,7 +101,7 @@ Reading file contents and computing cryptographic hashes for manifest generation
 ### scanner.go
 - **Types**
   - `Options struct` - Options for scanner behavior
-    - `IgnoreDotfiles bool`
+    - `IncludeDotfiles bool` - Include dot (hidden) files (excluded by default)
     - `FollowSymLinks bool`
   - `EnumerateStatus struct` - Progress information for enumeration phase
     - `FilesFound int64`
@@ -171,7 +171,7 @@ Reading file contents and computing cryptographic hashes for manifest generation
 ### manifest.go
 - **Types**
   - `ManifestScanOptions struct` - Options for scanning directories
-    - `IgnoreDotfiles bool`
+    - `IncludeDotfiles bool` - Include dot (hidden) files (excluded by default)
     - `FollowSymLinks bool`
 - **Functions**
   - `New() *manifest` - Creates a new empty manifest

contrib/usage.sh

@@ -15,5 +15,5 @@ trap cleanup EXIT
 echo "Building mfer..."
 go build -o "$TMPDIR/mfer" ./cmd/mfer
 
-"$TMPDIR/mfer" generate --ignore-dotfiles -o "$MANIFEST" .
+"$TMPDIR/mfer" generate -o "$MANIFEST" .
 "$TMPDIR/mfer" check --base . "$MANIFEST"

internal/cli/entry_test.go

@@ -8,6 +8,7 @@ import (
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 	urfcli "github.com/urfave/cli/v2"
+	"sneak.berlin/go/mfer/mfer"
 )
 
 func init() {
@@ -186,7 +187,7 @@ func TestUnknownCommand(t *testing.T) {
 	assert.Equal(t, 1, exitCode)
 }
 
-func TestGenerateWithIgnoreDotfiles(t *testing.T) {
+func TestGenerateExcludesDotfilesByDefault(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files including dotfiles
@@ -194,14 +195,39 @@ func TestGenerateWithIgnoreDotfiles(t *testing.T) {
 	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
 	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden", []byte("secret"), 0644))
 
-	// Generate manifest with --ignore-dotfiles
+	// Generate manifest without --include-dotfiles (default excludes dotfiles)
-	opts := testOpts([]string{"mfer", "-q", "generate", "--ignore-dotfiles", "-o", "/testdir/test.mf", "/testdir"}, fs)
+	opts := testOpts([]string{"mfer", "-q", "generate", "-o", "/testdir/test.mf", "/testdir"}, fs)
 	exitCode := RunWithOptions(opts)
 	require.Equal(t, 0, exitCode)
 
-	// Check that manifest exists and we can verify (hidden file won't cause failure even if missing)
+	// Check that manifest exists
 	exists, _ := afero.Exists(fs, "/testdir/test.mf")
 	assert.True(t, exists)
+
+	// Verify manifest only has 1 file (the non-dotfile)
+	manifest, err := mfer.NewManifestFromFile(fs, "/testdir/test.mf")
+	require.NoError(t, err)
+	assert.Len(t, manifest.Files(), 1)
+	assert.Equal(t, "file1.txt", manifest.Files()[0].Path)
+}
+
+func TestGenerateWithIncludeDotfiles(t *testing.T) {
+	fs := afero.NewMemMapFs()
+
+	// Create test files including dotfiles
+	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden", []byte("secret"), 0644))
+
+	// Generate manifest with --include-dotfiles
+	opts := testOpts([]string{"mfer", "-q", "generate", "--include-dotfiles", "-o", "/testdir/test.mf", "/testdir"}, fs)
+	exitCode := RunWithOptions(opts)
+	require.Equal(t, 0, exitCode)
+
+	// Verify manifest has 2 files (including dotfile)
+	manifest, err := mfer.NewManifestFromFile(fs, "/testdir/test.mf")
+	require.NoError(t, err)
+	assert.Len(t, manifest.Files(), 2)
 }
 
 func TestMultipleInputPaths(t *testing.T) {

internal/cli/freshen.go

@@ -40,7 +40,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 
 	basePath := ctx.String("base")
 	showProgress := ctx.Bool("progress")
-	ignoreDotfiles := ctx.Bool("IgnoreDotfiles")
+	includeDotfiles := ctx.Bool("IncludeDotfiles")
 	followSymlinks := ctx.Bool("FollowSymLinks")
 
 	// Find manifest file
@@ -112,7 +112,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 		}
 
 		// Handle dotfiles
-		if ignoreDotfiles && pathIsHidden(relPath) {
+		if !includeDotfiles && pathIsHidden(relPath) {
 			if info.IsDir() {
 				return filepath.SkipDir
 			}

internal/cli/gen.go

@@ -16,7 +16,7 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 	log.Debug("generateManifestOperation()")
 
 	opts := &scanner.Options{
-		IgnoreDotfiles: ctx.Bool("IgnoreDotfiles"),
+		IncludeDotfiles: ctx.Bool("IncludeDotfiles"),
 		FollowSymLinks:  ctx.Bool("FollowSymLinks"),
 		Fs:              mfa.Fs,
 	}

internal/cli/mfer.go

@@ -111,9 +111,9 @@ func (mfa *CLIApp) run(args []string) {
 						Usage:   "Resolve encountered symlinks",
 					},
 					&cli.BoolFlag{
-						Name:    "IgnoreDotfiles",
+						Name:    "IncludeDotfiles",
-						Aliases: []string{"ignore-dotfiles"},
+						Aliases: []string{"include-dotfiles"},
-						Usage:   "Ignore any dot (hidden) files encountered",
+						Usage:   "Include dot (hidden) files (excluded by default)",
 					},
 					&cli.StringFlag{
 						Name:    "output",
@@ -186,9 +186,9 @@ func (mfa *CLIApp) run(args []string) {
 						Usage:   "Resolve encountered symlinks",
 					},
 					&cli.BoolFlag{
-						Name:    "IgnoreDotfiles",
+						Name:    "IncludeDotfiles",
-						Aliases: []string{"ignore-dotfiles"},
+						Aliases: []string{"include-dotfiles"},
-						Usage:   "Ignore any dot (hidden) files encountered",
+						Usage:   "Include dot (hidden) files (excluded by default)",
 					},
 					&cli.BoolFlag{
 						Name:    "progress",

internal/scanner/scanner.go

@@ -42,7 +42,7 @@ type ScanStatus struct {
 
 // Options configures scanner behavior.
 type Options struct {
-	IgnoreDotfiles bool     // Skip files and directories starting with a dot
+	IncludeDotfiles bool     // Include files and directories starting with a dot (default: exclude)
 	FollowSymLinks  bool     // Resolve symlinks instead of skipping them
 	Fs              afero.Fs // Filesystem to use, defaults to OsFs if nil
 }
@@ -152,7 +152,7 @@ func (s *Scanner) enumerateFS(afs afero.Fs, basePath string, progress chan<- Enu
 		if err != nil {
 			return err
 		}
-		if s.options.IgnoreDotfiles && pathIsHidden(p) {
+		if !s.options.IncludeDotfiles && pathIsHidden(p) {
 			if info.IsDir() {
 				return filepath.SkipDir
 			}

mfer/manifest.go

@@ -41,7 +41,7 @@ func (m *manifest) String() string {
 
 // ManifestScanOptions configures behavior when scanning directories for manifest generation.
 type ManifestScanOptions struct {
-	IgnoreDotfiles bool // Skip files and directories starting with a dot
+	IncludeDotfiles bool // Include files and directories starting with a dot (default: exclude)
 	FollowSymLinks  bool // Resolve symlinks instead of skipping them
 }
 
@@ -153,7 +153,7 @@ func pathIsHidden(p string) bool {
 }
 
 func (m *manifest) addFile(p string, fi fs.FileInfo, sfsIndex int) error {
-	if m.scanOptions.IgnoreDotfiles && pathIsHidden(p) {
+	if !m.scanOptions.IncludeDotfiles && pathIsHidden(p) {
 		return nil
 	}
 	if fi != nil && fi.IsDir() {