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/freshen_test.go

@@ -413,6 +413,77 @@ 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.
+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))
+}
+
+// TestFreshenListsTargetOfTopIndexMFSymlink freshens a manifest kept
+// outside the directory --base names, after sub/index.mf is added there
+// and index.mf at the top is made a symlink to it: sub/index.mf is listed,
+// and the symlink, which freshen lists only with --follow-symlinks, is left
+// out like any index.mf at the top.
+func TestFreshenListsTargetOfTopIndexMFSymlink(t *testing.T) {
+	t.Parallel()
+
+	for name, flags := range map[string][]string{
+		"plain freshen":             nil,
+		"freshen --follow-symlinks": {testFlagFollowSymlinks},
+	} {
+		t.Run(name, func(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, testSubdirManifest), "an ordinary file")
+			require.NoError(t, os.Symlink(testSubdirManifest,
+				filepath.Join(tree, defaultManifestName)))
+
+			opts = testOpts(slices.Concat(
+				[]string{testApp, cmdFreshen, "-q"}, flags,
+				[]string{testFlagBase, tree, manifestPath},
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			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