Do not prepend paths starting with ~ or variable reference

bundle/config/mutator/prepend_workspace_prefix.go

@@ -45,6 +45,11 @@ func (m *prependWorkspacePrefix) Apply(ctx context.Context, b *bundle.Bundle) di
 				}
 
 				for _, prefix := range skipPrefixes {
+					// Skip prefixing if the path does not start with /, it might be variable reference or smth else.
+					if !strings.HasPrefix(path, "/") {
+						return pv, nil
+					}
+
 					if strings.HasPrefix(path, prefix) {
 						return pv, nil
 					}

bundle/config/mutator/prepend_workspace_prefix_test.go

@@ -31,6 +31,14 @@ func TestPrependWorkspacePrefix(t *testing.T) {
 			path:     "/Volumes/Users/test",
 			expected: "/Volumes/Users/test",
 		},
+		{
+			path:     "~/test",
+			expected: "~/test",
+		},
+		{
+			path:     "${workspace.file_path}/test",
+			expected: "${workspace.file_path}/test",
+		},
 	}
 
 	for _, tc := range testCases {