Never report index.mf at the top of the base as unlisted in check (closes #229)

gen and fetch write the manifest as index.mf at the top of the tree.
check left out only the manifest file it was given, so given a URL, or a
manifest stored elsewhere, it reported that index.mf as not in the
manifest, and --no-extra-files failed a tree fetch had just verified.
check now drops that one report for index.mf at the top of the base
directory. A manifest that lists index.mf still has it checked, and
index.mf in a subdirectory or fetch's leftover .index.mf.tmp are still
reported. The change is in package cli, which owns the default manifest
name; the Checker in package mfer is unchanged.

Model: opus-5-5

internal/cli/check.go

@@ -195,7 +195,10 @@ func countCheckFailures(
 
 // findExtraFiles reports files present on disk but absent from the
 // manifest, and anything the search cannot read: each is a failure, logged
-// at error level, under --no-extra-files, otherwise a warning.
+// at error level, under --no-extra-files, otherwise a warning. index.mf at
+// the top of the base directory is never reported as absent from the
+// manifest, since gen and fetch write the manifest there, even when check
+// is given another manifest or a URL.
 func findExtraFiles(
 	ctx context.Context, cmd *cli.Command, chk *mfer.Checker, failures *int64,
 ) error {
@@ -204,6 +207,10 @@ func findExtraFiles(
 
 	go func() {
 		for result := range extraResults {
+			if result.Status == mfer.StatusExtra && result.Path == defaultManifestName {
+				continue
+			}
+
 			if cmd.Bool("no-extra-files") {
 				*failures++
 

internal/cli/entry_test.go

@@ -1190,6 +1190,91 @@ func TestCheckURLManifestWithoutTempDirectory(t *testing.T) {
 	assert.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
 }
 
+// TestCheckNeverReportsIndexMfAtTopOfBase checks a tree holding index.mf at
+// its top, where gen and fetch write the manifest, against a manifest that
+// does not list it, given by URL and by a path outside the tree: the check
+// passes under --no-extra-files. index.mf in a subdirectory, and the temp
+// file fetch saves index.mf through, are still reported.
+func TestCheckNeverReportsIndexMfAtTopOfBase(t *testing.T) {
+	t.Parallel()
+
+	files := map[string][]byte{testFileTxt: []byte("hello")}
+	manifest := manifestOf(t, files)
+
+	server := httptest.NewServer(fetchTestHandler(manifest, files))
+	t.Cleanup(server.Close)
+
+	manifestOutsideTree := filepath.Join(t.TempDir(), "other.mf")
+	require.NoError(t, os.WriteFile(manifestOutsideTree, manifest, 0o600))
+
+	for name, manifestArg := range map[string]string{
+		"manifest by URL":  server.URL + "/" + defaultManifestName,
+		"manifest by path": manifestOutsideTree,
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			base := t.TempDir()
+			require.NoError(t, os.WriteFile(
+				filepath.Join(base, testFileTxt), files[testFileTxt], 0o600))
+			require.NoError(t, os.WriteFile(
+				filepath.Join(base, defaultManifestName), manifest, 0o600))
+
+			check := func() (int, string) {
+				opts := testOpts([]string{
+					testApp, cmdCheck, testFlagNoExtra, testFlagBase, base, manifestArg,
+				}, afero.NewOsFs())
+
+				return runCLI(opts), testStderr(t, opts)
+			}
+
+			exitCode, stderr := check()
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+
+			reported := []string{
+				testSubdir + "/" + defaultManifestName,
+				tempPathFor(defaultManifestName),
+			}
+
+			require.NoError(t, os.Mkdir(filepath.Join(base, testSubdir), 0o750))
+
+			for _, path := range reported {
+				require.NoError(t,
+					os.WriteFile(filepath.Join(base, path), manifest, 0o600))
+			}
+
+			exitCode, stderr = check()
+			assert.Equal(t, 1, exitCode, "stderr: %s", stderr)
+
+			for _, path := range reported {
+				assert.Contains(t, stderr, "EXTRA: "+path)
+			}
+		})
+	}
+}
+
+// TestCheckChecksListedIndexMf checks a tree against a manifest that lists
+// index.mf at the top of the tree, where that file has changed since: check
+// reports it like any other changed file.
+func TestCheckChecksListedIndexMf(t *testing.T) {
+	t.Parallel()
+
+	manifestPath := filepath.Join(t.TempDir(), "other.mf")
+	require.NoError(t, os.WriteFile(manifestPath, manifestOf(t, map[string][]byte{
+		defaultManifestName: []byte("listed"),
+	}), 0o600))
+
+	base := t.TempDir()
+	require.NoError(t, os.WriteFile(
+		filepath.Join(base, defaultManifestName), []byte("edited"), 0o600))
+
+	opts := testOpts([]string{
+		testApp, cmdCheck, testFlagBase, base, manifestPath,
+	}, afero.NewOsFs())
+	assert.Equal(t, 1, runCLI(opts), "stderr: %s", testStderr(t, opts))
+	assert.Contains(t, testStderr(t, opts), "HASH_MISMATCH: "+defaultManifestName)
+}
+
 // unlistableDirFs is a filesystem on which one directory cannot be listed.
 type unlistableDirFs struct {
 	afero.Fs