diff --git a/apps/files/js/file-upload.js b/apps/files/js/file-upload.js
index eb57101f07d7..23f1deb0a47f 100644
--- a/apps/files/js/file-upload.js
+++ b/apps/files/js/file-upload.js
@@ -37,12 +37,11 @@ OC.FileUpload = function(uploader, data) {
 	if (!data) {
 		throw 'Missing "data" argument in OC.FileUpload constructor';
 	}
-	var path = '';
+	var basePath = '';
 	if (this.uploader.fileList) {
-		path = OC.joinPaths(this.uploader.fileList.getCurrentDirectory(), this.getFile().name);
-	} else {
-		path = this.getFile().name;
+		basePath = this.uploader.fileList.getCurrentDirectory();
 	}
+	var path = OC.joinPaths(basePath, this.getFile().relativePath || '', this.getFile().name);
 	this.id = 'web-file-upload-' + md5(path) + '-' + (new Date()).getTime();
 };
 OC.FileUpload.CONFLICT_MODE_DETECT = 0;
@@ -622,7 +621,13 @@ OC.Uploader.prototype = _.extend({
 	 * Clear uploads
 	 */
 	clear: function() {
-		this._uploads = {};
+		var remainingUploads = {};
+		_.each(this._uploads, function(upload, key) {
+			if (!upload.isDone) {
+				remainingUploads[key] = upload;
+			}
+		});
+		this._uploads = remainingUploads;
 		this._knownDirs = {};
 	},
 	/**
@@ -1092,6 +1097,7 @@ OC.Uploader.prototype = _.extend({
 					var upload = self.getUpload(data);
 					var that = $(this);
 					self.log('done', e, upload);
+					upload.isDone = true;
 
 					var status = upload.getResponseStatus();
 					if (status < 200 || status >= 300) {
diff --git a/apps/files/js/upload.js b/apps/files/js/upload.js
deleted file mode 100644
index 518608615e06..000000000000
--- a/apps/files/js/upload.js
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * Copyright (c) 2014
- *
- * This file is licensed under the Affero General Public License version 3
- * or later.
- *
- * See the COPYING-README file.
- *
- */
-
-function Upload(fileSelector) {
-	if ($.support.xhrFileUpload) {
-		return new XHRUpload(fileSelector.target.files);
-	} else {
-		return new FormUpload(fileSelector);
-	}
-}
-Upload.target = OC.filePath('files', 'ajax', 'upload.php');
diff --git a/apps/files/tests/js/fileUploadSpec.js b/apps/files/tests/js/fileUploadSpec.js
index 946ac2a8cc45..82c6b6ca7b51 100644
--- a/apps/files/tests/js/fileUploadSpec.js
+++ b/apps/files/tests/js/fileUploadSpec.js
@@ -119,6 +119,16 @@ describe('OC.Upload tests', function() {
 			expect(upload).toBeDefined();
 			expect(upload.getFileName()).toEqual('test.txt');
 		});
+		it('clear leaves pending uploads', function() {
+			uploader._uploads = {
+				'abc': {name: 'a job well done.txt', isDone: true},
+				'def': {name: 'whatevs.txt'}
+			};
+
+			uploader.clear();
+
+			expect(uploader._uploads).toEqual({'def': {name: 'whatevs.txt'}});
+		});
 	});
 	describe('Upload conflicts', function() {
 		var conflictDialogStub;