Fix all linter errors

- Add explicit error ignoring with _ = for Close/Remove calls
- Rename WriteTo to Write to avoid io.WriterTo interface conflict
- Fix errcheck warnings in fetch, freshen, gen, mfer, checker,
  deserialize, serialize, and output files

internal/cli/gen.go

@@ -76,7 +76,7 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 	if err != nil {
 		return fmt.Errorf("failed to create output file: %w", err)
 	}
-	defer outFile.Close()
+	defer func() { _ = outFile.Close() }()
 
 	// Phase 2: Scan - read file contents and generate manifest
 	var scanProgress chan scanner.ScanStatus