- Fix error syncing empty files

- Clarify quota message to say that metadata will continue to sync
- Fix some other problem that I don't remember

chrome/content/zotero/xpcom/data/item.js

@@ -2563,7 +2563,7 @@ Zotero.Item.prototype.getFilename = function () {
  *
  * -1   		Destination file exists -- use _force_ to overwrite
  * -2		Error renaming
- * false		Attachment file not found or other error
+ * false		Attachment file not found
  */
 Zotero.Item.prototype.renameAttachmentFile = function(newName, overwrite) {
 	var file = this.getFile();
@@ -2591,10 +2591,16 @@ Zotero.Item.prototype.renameAttachmentFile = function(newName, overwrite) {
 		
 		file.moveTo(null, newName);
 		// Update mod time and clear hash so the file syncs
+		// TODO: use an integer counter instead of mod time for change detection
 		dest.lastModifiedTime = new Date();
 		this.relinkAttachmentFile(dest);
 		
+		Zotero.DB.beginTransaction();
+		
 		Zotero.Sync.Storage.setSyncedHash(this.id, null, false);
+		Zotero.Sync.Storage.setSyncState(this.id, Zotero.Sync.Storage.SYNC_STATE_TO_UPLOAD);
+		
+		Zotero.DB.commitTransaction();
 		
 		return true;
 	}

chrome/content/zotero/xpcom/storage/zfs.js

@@ -164,7 +164,7 @@ Zotero.Sync.Storage.Session.ZFS.prototype.downloadFile = function (request) {
 					return;
 				}
 				// If not compressed, check hash, in case only timestamp changed
-				else if (!info.compressed && Zotero.Utilities.prototype.md5(file) == syncHash) {
+				else if (!info.compressed && item.attachmentHash == syncHash) {
 					Zotero.debug("File hash matches remote file -- skipping download");
 					
 					Zotero.DB.beginTransaction();

chrome/content/zotero/xpcom/sync.js

@@ -39,16 +39,24 @@ Zotero.Sync = new function() {
 	
 	
 	this.init = function () {
+		Zotero.DB.beginTransaction();
+		
 		var sql = "SELECT version FROM version WHERE schema='syncdeletelog'";
 		if (!Zotero.DB.valueQuery(sql)) {
 			sql = "SELECT COUNT(*) FROM syncDeleteLog";
 			if (Zotero.DB.valueQuery(sql)) {
 				throw ('syncDeleteLog not empty and no timestamp in Zotero.Sync.delete()');
 			}
+			
+			var syncInitTime = Zotero.DB.transactionDate;
+			syncInitTime = Zotero.Date.toUnixTimestamp(syncInitTime);
+			
 			sql = "INSERT INTO version VALUES ('syncdeletelog', ?)";
-			Zotero.DB.query(sql, Zotero.Date.getUnixTimestamp());
+			Zotero.DB.query(sql, syncInitTime);
 		}
 		
+		Zotero.DB.commitTransaction();
+		
 		this.EventListener.init();
 	}
 	
@@ -136,6 +144,10 @@ Zotero.Sync = new function() {
 		}
 		
 		// Last sync time is before start of log
+		Zotero.debug('==============');
+		Zotero.debug(lastSyncDate);
+		Zotero.debug(lastSyncDate + '');
+		Zotero.debug(syncLogStart);
 		if (lastSyncDate && new Date(syncLogStart * 1000) > lastSyncDate) {
 			return -1;
 		}
@@ -716,7 +728,8 @@ Zotero.Sync.Runner = new function () {
 		if (e) {
 			if (e.error == Zotero.Error.ERROR_ZFS_OVER_QUOTA) {
 				// TODO: localize
-				message = "You have reached your Zotero File Storage quota. Some files were not synced.\n\n"
+				message = "You have reached your Zotero File Storage quota. Some files were not synced. "
+							+ "Other Zotero data will continue to sync to the server.\n\n"
 							+ "See your zotero.org account settings for additional storage options.";
 				
 				buttonText = "Open Account Settings";

chrome/content/zotero/xpcom/utilities.js

@@ -415,6 +415,12 @@ Zotero.Utilities.prototype.md5 = function(strOrFile, base64) {
 		ch.update(data, data.length);
 	}
 	else if (strOrFile instanceof Components.interfaces.nsIFile) {
+		// Otherwise throws (NS_ERROR_NOT_AVAILABLE) [nsICryptoHash.updateFromStream]
+		if (!strOrFile.fileSize) {
+			// MD5 for empty string
+			return "d41d8cd98f00b204e9800998ecf8427e";
+		}
+		
 		var istream = Components.classes["@mozilla.org/network/file-input-stream;1"]
 						.createInstance(Components.interfaces.nsIFileInputStream);
 		// open for reading