Never list index.mf at the top of the tree in gen and freshen (closes #233)

fetch saves the manifest as index.mf at the top of the tree and refuses a
manifest that lists a file there. gen given --output, and freshen with its
manifest outside the base directory, listed such a file, so they wrote
manifests fetch would not take.

gen now leaves out index.mf in each directory it is given, or beside each
file it is given, the same way it leaves out the file it writes. freshen
leaves out index.mf at the top of the base directory. index.mf in a
subdirectory is still listed. The README says so for both commands.

Model: opus-5-5

internal/cli/entry_test.go

@@ -1420,6 +1420,66 @@ func TestGenerateLeavesLeftoverTempFileOutOfListing(t *testing.T) {
 	assert.Equal(t, []string{testFileTxt}, manifestPaths(t, fs, output))
 }
 
+// TestGenerateLeavesTopIndexMFOutOfListing runs gen with --output outside
+// the paths it is given: index.mf at the top of each directory given, and
+// a file given by that name, are not listed, since fetch saves the manifest
+// as index.mf at the top of the tree, while sub/index.mf is listed. The
+// files are recognized by file identity, which needs the real filesystem.
+func TestGenerateLeavesTopIndexMFOutOfListing(t *testing.T) {
+	t.Parallel()
+
+	// Paths are relative to a temp dir holding tree, which holds file.txt,
+	// index.mf and sub/index.mf, and second, which holds second.txt and
+	// index.mf.
+	for name, tc := range map[string]struct {
+		paths  []string
+		listed []string
+	}{
+		"directory": {
+			[]string{"tree"},
+			[]string{testFileTxt, testSubdirManifest},
+		},
+		"two directories": {
+			[]string{"tree", "second"},
+			[]string{testFileTxt, testSubdirManifest, "second.txt"},
+		},
+		"files": {
+			[]string{"tree/" + testFileTxt, "tree/" + defaultManifestName},
+			[]string{testFileTxt},
+		},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			root := t.TempDir()
+			tree := filepath.Join(root, "tree")
+			second := filepath.Join(root, "second")
+
+			fs := afero.NewOsFs()
+			require.NoError(t, fs.MkdirAll(filepath.Join(tree, testSubdir), 0o750))
+			require.NoError(t, fs.MkdirAll(second, 0o750))
+			writeTestFile(t, fs, filepath.Join(tree, testFileTxt), "hello")
+			writeTestFile(t, fs, filepath.Join(tree, defaultManifestName), "an ordinary file")
+			writeTestFile(t, fs, filepath.Join(tree, testSubdirManifest), "an ordinary file")
+			writeTestFile(t, fs, filepath.Join(second, "second.txt"), "second")
+			writeTestFile(t, fs, filepath.Join(second, defaultManifestName), "an ordinary file")
+
+			paths := make([]string, 0, len(tc.paths))
+			for _, path := range tc.paths {
+				paths = append(paths, filepath.Join(root, path))
+			}
+
+			output := filepath.Join(root, "other.mf")
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdGenerate, "-q", "-o", output}, paths,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assert.ElementsMatch(t, tc.listed, manifestPaths(t, fs, output))
+		})
+	}
+}
+
 // writeTestTree writes file.txt and sub/nested.txt under dir.
 func writeTestTree(t *testing.T, fs afero.Fs, dir string) {
 	t.Helper()

internal/cli/freshen.go

@@ -411,12 +411,17 @@ func (mfa *CLIApp) freshenScan(
 	startScan := time.Now()
 	showProgress := cmd.Bool("progress")
 
-	// Leave out the manifest and a temp file left by an interrupted run,
-	// as gen does. A path that cannot be stat'd, normally because no file
-	// is there, needs no leaving out.
+	// Leave out the manifest, a temp file left by an interrupted run, and
+	// index.mf at the top of the base directory, where fetch saves the
+	// manifest, as gen does. A path that cannot be stat'd, normally because
+	// no file is there, needs no leaving out.
 	var excluded []fs.FileInfo
 
-	for _, p := range []string{manifestPath, manifestTempPath(manifestPath)} {
+	for _, p := range []string{
+		manifestPath,
+		manifestTempPath(manifestPath),
+		filepath.Join(absBase, defaultManifestName),
+	} {
 		info, err := mfa.Fs.Stat(p)
 		if err == nil {
 			excluded = append(excluded, info)

internal/cli/freshen_test.go

@@ -413,6 +413,34 @@ func TestFreshenLeavesLeftoverTempFileOutOfListing(t *testing.T) {
 		manifestPaths(t, fs, manifestPath))
 }
 
+// TestFreshenLeavesTopIndexMFOutOfListing freshens a manifest kept outside
+// the directory --base names, after index.mf and sub/index.mf are added
+// there: index.mf at the top is not listed, since fetch saves the manifest
+// there, while sub/index.mf is listed. The file is recognized by file
+// identity, which needs the real filesystem.
+func TestFreshenLeavesTopIndexMFOutOfListing(t *testing.T) {
+	t.Parallel()
+
+	root := t.TempDir()
+	tree := filepath.Join(root, "tree")
+	manifestPath := filepath.Join(root, "other.mf")
+
+	fs := afero.NewOsFs()
+	require.NoError(t, fs.MkdirAll(filepath.Join(tree, testSubdir), 0o750))
+	writeTestFile(t, fs, filepath.Join(tree, testFileTxt), "hello")
+
+	opts := testOpts([]string{testApp, cmdGenerate, "-q", "-o", manifestPath, tree}, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	writeTestFile(t, fs, filepath.Join(tree, defaultManifestName), "an ordinary file")
+	writeTestFile(t, fs, filepath.Join(tree, testSubdirManifest), "an ordinary file")
+
+	runFreshen(t, fs, tree, manifestPath)
+
+	assert.ElementsMatch(t, []string{testFileTxt, testSubdirManifest},
+		manifestPaths(t, fs, manifestPath))
+}
+
 // TestFreshenResolvesEntriesAgainstManifestDirectory adds sub/c.txt, then
 // runs freshen from the directory above sub, on the manifest in sub.
 // Without --base, the manifest then lists the files in sub, whether freshen

internal/cli/gen.go

@@ -111,15 +111,19 @@ func (mfa *CLIApp) outputPath(cmd *cli.Command) (string, error) {
 		return defaultManifestName, nil
 	}
 
-	arg := cmd.Args().First()
+	return mfa.topIndexMFPath(cmd.Args().First()), nil
+}
 
+// topIndexMFPath returns index.mf in the directory path names, or beside
+// the file it names, which is the top of the tree gen lists for that path.
+func (mfa *CLIApp) topIndexMFPath(path string) string {
 	// A path that does not exist is refused when it is enumerated.
-	info, err := mfa.Fs.Stat(arg)
+	info, err := mfa.Fs.Stat(path)
 	if err == nil && !info.IsDir() {
-		return filepath.Join(filepath.Dir(arg), defaultManifestName), nil
+		return filepath.Join(filepath.Dir(path), defaultManifestName)
 	}
 
-	return filepath.Join(arg, defaultManifestName), nil
+	return filepath.Join(path, defaultManifestName)
 }
 
 // buildScannerOptions constructs scanner options from the CLI flags and
@@ -139,6 +143,18 @@ func (mfa *CLIApp) buildScannerOptions(
 		ExcludePaths: []string{output, manifestTempPath(output)},
 	}
 
+	// Nor does index.mf at the top of the tree, since fetch saves the
+	// manifest there and refuses a manifest that lists it. With no path
+	// given, gen lists the current directory.
+	paths := cmd.Args().Slice()
+	if len(paths) == 0 {
+		paths = []string{"."}
+	}
+
+	for _, path := range paths {
+		opts.ExcludePaths = append(opts.ExcludePaths, mfa.topIndexMFPath(path))
+	}
+
 	// Set seed for deterministic UUID if provided
 	if seed := cmd.String("seed"); seed != "" {
 		opts.Seed = seed