Normalise paths to ensure they are compared properly

core/index.go

@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"io"
 	"os"
+	"path"
 	"path/filepath"
 	"sort"
 	"strings"
@@ -261,6 +262,11 @@ func (in *Index) Refresh() error {
 		),
 	)
 
+	// Normalise file paths: updateFile needs to compare path equality
+	for i := range in.Files {
+		in.Files[i].File = path.Clean(in.Files[i].File)
+	}
+
 	for _, v := range fileList {
 		start := time.Now()