Default the manifest to index.mf and keep it out of its own listing (closes #100)

mfer gen now writes index.mf instead of .index.mf, the name fetch
requests and the README calls the standard filename. Given a
directory, check, freshen, list and export look only for index.mf;
.index.mf is no longer recognized. Because index.mf is not hidden, the
scanner now leaves the output file out of the listing by its path: gen
--force over an existing manifest no longer lists the old one, while a
file named index.mf in a subdirectory is still listed.

Model: opus-5-5

internal/cli/entry_test.go

@@ -638,6 +638,43 @@ func TestGenerateFailsWithoutForceWhenOutputExists(t *testing.T) {
 	assert.Equal(t, "existing", string(content), "original file should be preserved")
 }
 
+// TestGenerateLeavesOutputOutOfListing overwrites an output file inside the
+// scanned tree with --force: the old file is not listed, while a file named
+// index.mf in a subdirectory still is.
+func TestGenerateLeavesOutputOutOfListing(t *testing.T) {
+	t.Parallel()
+
+	for name, output := range map[string]string{
+		"default name":                 "/testdir/index.mf",
+		"other name in a subdirectory": "/testdir/sub/listing.mf",
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			fs := afero.NewMemMapFs()
+			require.NoError(t, fs.MkdirAll("/testdir/sub", 0o755))
+			writeTestFile(t, fs, "/testdir/readme.txt", "hello")
+			writeTestFile(t, fs, "/testdir/sub/index.mf", "an ordinary file")
+			writeTestFile(t, fs, output, "previous manifest")
+
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", "--force", "-o", output, testDir,
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			manifest, err := mfer.NewManifestFromFile(fs, output)
+			require.NoError(t, err)
+
+			paths := make([]string, 0, len(manifest.Files()))
+			for _, f := range manifest.Files() {
+				paths = append(paths, f.GetPath())
+			}
+
+			assert.ElementsMatch(t, []string{"readme.txt", "sub/index.mf"}, paths)
+		})
+	}
+}
+
 func TestGenerateAtomicWriteUsesTemp(t *testing.T) {
 	t.Parallel()