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++