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.

Both now leave out each file the manifest would list as index.mf: one at
the top of the tree, or a file given to gen by that name. The rule goes by
that path alone and looks up no file, so a symlink named index.mf never
hides the file it points to. index.mf in a subdirectory is still listed.
The scanner in package mfer gets an option to leave out files by the path
they would be listed by.

Model: opus-5-5

internal/cli/entry_test.go

@@ -27,19 +27,20 @@ import (
 )
 
 const (
-	testApp         = "mfer"
-	testGitrev      = "abc123"
-	testDir         = "/testdir"
-	testFile1       = "/testdir/file1.txt"
-	testMF          = "/testdir/test.mf"
-	testOutput      = "/output.mf"
-	testManifest    = "/manifest.mf"
-	testFlagBase    = "--base"
-	testFlagNoExtra = "--no-extra-files"
-	testFlagVersion = "--version"
-	testFlagVerbose = "--verbose"
-	testFlagHelp    = "--help"
-	testCmdHelp     = "help"
+	testApp                = "mfer"
+	testGitrev             = "abc123"
+	testDir                = "/testdir"
+	testFile1              = "/testdir/file1.txt"
+	testMF                 = "/testdir/test.mf"
+	testOutput             = "/output.mf"
+	testManifest           = "/manifest.mf"
+	testFlagBase           = "--base"
+	testFlagNoExtra        = "--no-extra-files"
+	testFlagFollowSymlinks = "--follow-symlinks"
+	testFlagVersion        = "--version"
+	testFlagVerbose        = "--verbose"
+	testFlagHelp           = "--help"
+	testCmdHelp            = "help"
 )
 
 var errSimulatedWrite = errors.New("simulated write failure")
@@ -1002,7 +1003,7 @@ func TestCheckReportsUnlistedSymlinkToFileOnly(t *testing.T) {
 		exitCode int
 		extras   []string // what check reports as not in the manifest
 	}{
-		"gen --follow-symlinks": {[]string{"--follow-symlinks"}, 0, nil},
+		"gen --follow-symlinks": {[]string{testFlagFollowSymlinks}, 0, nil},
 		"plain gen":             {nil, 1, []string{"filelink"}},
 	} {
 		t.Run(name, func(t *testing.T) {
@@ -1567,6 +1568,141 @@ 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.
+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))
+		})
+	}
+}
+
+// TestGenerateListsTargetOfTopIndexMFSymlink makes index.mf at the top of
+// the tree a symlink to another file in it, and runs gen with --output
+// outside the tree: the file it points to is listed under its own name,
+// and the symlink, which gen lists only with --follow-symlinks, is left out
+// like any index.mf at the top of the tree.
+func TestGenerateListsTargetOfTopIndexMFSymlink(t *testing.T) {
+	t.Parallel()
+
+	// Paths are relative to tree, which holds file.txt, sub/index.mf and
+	// index.mf, a symlink to target.
+	for name, tc := range map[string]struct {
+		target string
+		flags  []string
+		path   string // the path gen is given
+		listed []string
+	}{
+		"directory given": {
+			testSubdirManifest, nil, ".",
+			[]string{testFileTxt, testSubdirManifest},
+		},
+		"directory given, --follow-symlinks": {
+			testSubdirManifest,
+			[]string{testFlagFollowSymlinks},
+			".",
+			[]string{testFileTxt, testSubdirManifest},
+		},
+		"file given": {
+			testFileTxt, nil, testFileTxt,
+			[]string{testFileTxt},
+		},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			root := t.TempDir()
+			tree := filepath.Join(root, "tree")
+
+			fs := afero.NewOsFs()
+			require.NoError(t, fs.MkdirAll(filepath.Join(tree, testSubdir), 0o750))
+			writeTestFile(t, fs, filepath.Join(tree, testFileTxt), "hello")
+			writeTestFile(t, fs, filepath.Join(tree, testSubdirManifest), "an ordinary file")
+			require.NoError(t,
+				os.Symlink(tc.target, filepath.Join(tree, defaultManifestName)))
+
+			output := filepath.Join(root, "other.mf")
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdGenerate, "-q", "-o", output}, tc.flags,
+				[]string{filepath.Join(tree, tc.path)},
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assert.ElementsMatch(t, tc.listed, manifestPaths(t, fs, output))
+		})
+	}
+}
+
+// TestGenerateListsIndexMFBesideFileGiven runs gen with --output outside
+// the tree, given sub/b.txt and the tree: sub/index.mf, beside the file
+// given, is listed, since a file given is left out only when its own name
+// is index.mf.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestGenerateListsIndexMFBesideFileGiven(t *testing.T) {
+	setupManifestInSubdir(t)
+
+	fs := afero.NewOsFs()
+	output := filepath.Join(t.TempDir(), "other.mf")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", "-o", output, filepath.Join(testSubdir, "b.txt"), ".",
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	assert.Contains(t, manifestPaths(t, fs, output), testSubdirManifest)
+}
+
 // writeTestTree writes file.txt and sub/nested.txt under dir.
 func writeTestTree(t *testing.T, fs afero.Fs, dir string) {
 	t.Helper()