fix: FindExtraFiles skips dotfiles and manifest files to avoid false positives

FindExtraFiles now skips hidden files/directories and manifest files
(index.mf, .index.mf) when looking for extra files. Previously it would
report these as 'extra' even though they are intentionally excluded from
manifests by default, making --no-extra-files unusable.

Also includes IsHiddenPath fix for '.' (needed by the new filtering).

internal/checker/checker.go

@@ -227,12 +227,14 @@ func (c *Checker) checkFile(entry *mfer.MFFilePath, checkedBytes *int64) Result
 
 // FindExtraFiles walks the filesystem and reports files not in the manifest.
 // Results are sent to the results channel. The channel is closed when done.
+// Hidden files/directories (starting with .) are skipped, as they are excluded
+// from manifests by default. The manifest file itself is also skipped.
 func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) error {
 	if results != nil {
 		defer close(results)
 	}
 
-	return afero.Walk(c.fs, c.basePath, func(path string, info os.FileInfo, err error) error {
+	return afero.Walk(c.fs, c.basePath, func(walkPath string, info os.FileInfo, err error) error {
 		if err != nil {
 			return err
 		}
@@ -243,15 +245,29 @@ func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) err
 		default:
 		}
 
+		// Get relative path
+		relPath, err := filepath.Rel(c.basePath, walkPath)
+		if err != nil {
+			return err
+		}
+
+		// Skip hidden files and directories (dotfiles)
+		if mfer.IsHiddenPath(filepath.ToSlash(relPath)) {
+			if info.IsDir() {
+				return filepath.SkipDir
+			}
+			return nil
+		}
+
 		// Skip directories
 		if info.IsDir() {
 			return nil
 		}
 
-		// Get relative path
-		relPath, err := filepath.Rel(c.basePath, path)
-		if err != nil {
-			return err
+		// Skip manifest files
+		base := filepath.Base(relPath)
+		if base == "index.mf" || base == ".index.mf" {
+			return nil
 		}
 
 		// Check if path is in manifest