diff --git a/src/js/dao/email-dao.js b/src/js/dao/email-dao.js
index e826d72..6138a0f 100644
--- a/src/js/dao/email-dao.js
+++ b/src/js/dao/email-dao.js
@@ -6,6 +6,16 @@ define(function(require) {
         config = require('js/app-config').config,
         str = require('js/app-config').string;
 
+    /**
+     * High-level data access object that orchestrates everything around the handling of encrypted mails:
+     * PGP de-/encryption, receiving via IMAP, sending via SMTP, MIME parsing, local db persistence
+     *
+     * @param {Object} keychain The keychain DAO handles keys transparently
+     * @param {Object} crypto Orchestrates decryption
+     * @param {Object} devicestorage Handles persistence to the local indexed db
+     * @param {Object} pgpbuilder Generates and encrypts MIME and SMTP messages
+     * @param {Object} mailreader Parses MIME messages received from IMAP
+     */
     var EmailDAO = function(keychain, crypto, devicestorage, pgpbuilder, mailreader) {
         this._keychain = keychain;
         this._crypto = crypto;
@@ -22,6 +32,16 @@ define(function(require) {
     //
 
 
+    /**
+     * Initializes the email dao:
+     * - validates the email address
+     * - retrieves the user's key pair (if available)
+     * - initializes _account.folders with the content from memory
+     *
+     * @param {Object} options.account The account
+     * @param {String} options.account.emailAddress The user's id
+     * @param {Function} callback(error, keypair) Invoked with the keypair or error information when the email dao is initialized
+     */
     EmailDAO.prototype.init = function(options, callback) {
         var self = this,
             keypair;
@@ -70,6 +90,11 @@ define(function(require) {
         }
     };
 
+    /**
+     * Unlocks the keychain by either decrypting an existing private key or generating a new keypair
+     * @param {String} options.passphrase The passphrase to decrypt the private key
+     * @param {Function} callback(error) Invoked when the the keychain is unlocked or when an error occurred buring unlocking
+     */
     EmailDAO.prototype.unlock = function(options, callback) {
         var self = this;
 
@@ -170,6 +195,14 @@ define(function(require) {
         }
     };
 
+    /**
+     * Opens a folder in IMAP so that we can receive updates for it.
+     * Please note that this is a no-op if you try to open the outbox, since it is not an IMAP folder
+     * but a virtual folder that only exists on disk.
+     *
+     * @param {Object} options.folder The folder to be opened
+     * @param {Function} callback(error) Invoked when the folder has been opened
+     */
     EmailDAO.prototype.openFolder = function(options, callback) {
         var self = this,
             err;
@@ -190,6 +223,14 @@ define(function(require) {
         }, callback);
     };
 
+    /**
+     * Synchronizes a folder's contents from disk to memory, i.e. if
+     * a message has disappeared from the disk, this method will remove it from folder.messages, and
+     * it adds any messages from disk to memory the are not yet in folder.messages
+     *
+     * @param {Object} options.folder The folder to synchronize
+     * @param {Function} callback [description]
+     */
     EmailDAO.prototype.refreshFolder = function(options, callback) {
         var self = this,
             folder = options.folder;
@@ -205,8 +246,8 @@ define(function(require) {
 
             var storedUids = _.pluck(storedMessages, 'uid'),
                 memoryUids = _.pluck(folder.messages, 'uid'),
-                newUids = _.difference(storedUids, memoryUids),
-                removedUids = _.difference(memoryUids, storedUids);
+                newUids = _.difference(storedUids, memoryUids), // uids of messages that are not yet in memory
+                removedUids = _.difference(memoryUids, storedUids); // uids of messages that are no longer stored on the disk
 
             // which messages are new on the disk that are not yet in memory?
             _.filter(storedMessages, function(msg) {
@@ -240,6 +281,15 @@ define(function(require) {
         }
     };
 
+    /**
+     * Fetches a message's headers from IMAP.
+     *
+     * NB! If we fetch a message whose subject line correspond's to that of a verification message,
+     * we try to verify that, and if that worked, we delete the verified message from IMAP.
+     *
+     * @param {Object} options.folder The folder for which to fetch the message
+     * @param {Function} callback(error) Invoked when the message is persisted and added to folder.messages
+     */
     EmailDAO.prototype.fetchMessages = function(options, callback) {
         var self = this,
             folder = options.folder;
@@ -328,6 +378,7 @@ define(function(require) {
             callback(err);
         }
 
+        // Handles verification of public keys, deletion of messages with verified keys
         function handleVerification(message, localCallback) {
             self._getBodyParts({
                 folder: folder,
@@ -375,6 +426,17 @@ define(function(require) {
         }
     };
 
+    /**
+     * Delete a message from IMAP, disk and folder.messages.
+     *
+     * Please note that this deletes from disk only if you delete from the outbox,
+     * since it is not an IMAP folder but a virtual folder that only exists on disk.
+     *
+     * @param {Object} options.folder The folder from which to delete the messages
+     * @param {Object} options.message The message that should be deleted
+     * @param {Boolean} options.localOnly Indicated if the message should not be removed from IMAP
+     * @param {Function} callback(error) Invoked when the message was delete, or an error occurred
+     */
     EmailDAO.prototype.deleteMessage = function(options, callback) {
         var self = this,
             folder = options.folder,
@@ -384,6 +446,7 @@ define(function(require) {
 
         folder.messages.splice(folder.messages.indexOf(message), 1);
 
+        // delete only locally
         if (options.localOnly || options.folder.path === config.outboxMailboxPath) {
             deleteLocal();
             return;
@@ -393,6 +456,7 @@ define(function(require) {
 
         function deleteImap() {
             if (!self._account.online) {
+                // no action if we're not online
                 done({
                     errMsg: 'Client is currently offline!',
                     code: 42
@@ -400,6 +464,7 @@ define(function(require) {
                 return;
             }
 
+            // delete from IMAP
             self._imapDeleteMessage({
                 folder: folder,
                 uid: message.uid
@@ -414,6 +479,7 @@ define(function(require) {
         }
 
         function deleteLocal() {
+            // delete from indexed db
             self._localDeleteMessage({
                 folder: folder,
                 uid: message.uid
@@ -430,24 +496,37 @@ define(function(require) {
         }
     };
 
+    /**
+     * Updates a message's 'unread' and 'answered' flags
+     *
+     * Please note if you set flags on disk only if you delete from the outbox,
+     * since it is not an IMAP folder but a virtual folder that only exists on disk.
+     * 
+     * @param {[type]} options [description]
+     * @param {Function} callback [description]
+     */
     EmailDAO.prototype.setFlags = function(options, callback) {
         var self = this,
             folder = options.folder,
             message = options.message;
 
-        self._account.busy = true;
+        self._account.busy = true; // start the spinner
 
+        // no-op if the message if not present anymore (for whatever reason)
         if (folder.messages.indexOf(message) < 0) {
             self._account.busy = false; // stop the spinner
             return;
         }
 
+        // don't do a roundtrip to IMAP,
+        // especially if you want to mark outbox messages 
         if (options.localOnly || options.folder.path === config.outboxMailboxPath) {
             markStorage();
             return;
         }
 
         if (!self._account.online) {
+            // no action if we're not online
             done({
                 errMsg: 'Client is currently offline!',
                 code: 42
@@ -458,6 +537,7 @@ define(function(require) {
         markImap();
 
         function markImap() {
+            // mark a message unread/answered on IMAP
             self._imapMark({
                 folder: folder,
                 uid: options.message.uid,
@@ -474,6 +554,9 @@ define(function(require) {
         }
 
         function markStorage() {
+            // angular pollutes that data transfer objects with helper properties (e.g. $$hashKey),
+            // which we do not want to persist to disk. in order to avoid that, we load the pristine
+            // message from disk, change the flags and re-persist it to disk
             self._localListMessages({
                 folder: folder,
                 uid: options.message.uid,
@@ -483,10 +566,13 @@ define(function(require) {
                     return;
                 }
 
+                // set the flags
                 var storedMessage = storedMessages[0];
                 storedMessage.unread = options.message.unread;
                 storedMessage.answered = options.message.answered;
+                storedMessage.modseq = options.message.modseq || storedMessage.modseq;
 
+                // store
                 self._localStoreMessages({
                     folder: folder,
                     emails: [storedMessage]
@@ -663,6 +749,14 @@ define(function(require) {
         }
     };
 
+    /**
+     * Retrieves an attachment matching a body part for a given uid and a folder
+     *
+     * @param {Object} options.folder The folder where to find the attachment
+     * @param {Number} options.uid The uid for the message the attachment body part belongs to
+     * @param {Object} options.attachment The attachment body part to fetch and parse from IMAP
+     * @param {Function} callback(error, attachment) Invoked when the attachment body part was retrieved and parsed, or an error occurred
+     */
     EmailDAO.prototype.getAttachment = function(options, callback) {
         this._getBodyParts({
             folder: options.folder,
@@ -674,11 +768,19 @@ define(function(require) {
                 return;
             }
 
+            // add the content to the original object
             options.attachment.content = parsedBodyParts[0].content;
             callback(err, err ? undefined : options.attachment);
         });
     };
 
+    /**
+     * Decrypts a message and replaces sets the decrypted plaintext as the message's body, html, or attachment, respectively.
+     * The first encrypted body part's ciphertext (in the content property) will be decrypted.
+     *
+     * @param {Object} options.message The message
+     * @param {Function} callback(error, message)
+     */
     EmailDAO.prototype.decryptBody = function(options, callback) {
         var self = this,
             message = options.message;
@@ -762,6 +864,12 @@ define(function(require) {
         }
     };
 
+    /**
+     * Encrypted (if necessary) and sends a message with a predefined clear text greeting.
+     *
+     * @param {Object} options.email The message to be sent
+     * @param {Function} callback(error) Invoked when the message was sent, or an error occurred
+     */
     EmailDAO.prototype.sendEncrypted = function(options, callback) {
         var self = this;
 
@@ -782,6 +890,12 @@ define(function(require) {
         }, callback);
     };
 
+    /**
+     * Sends a signed message in the plain
+     *
+     * @param {Object} options.email The message to be sent
+     * @param {Function} callback(error) Invoked when the message was sent, or an error occurred
+     */
     EmailDAO.prototype.sendPlaintext = function(options, callback) {
         if (!this._account.online) {
             callback({
@@ -797,6 +911,12 @@ define(function(require) {
         }, callback);
     };
 
+    /**
+     * Signs and encrypts a message
+     *
+     * @param {Object} options.email The message to be encrypted
+     * @param {Function} callback(error, message) Invoked when the message was encrypted, or an error occurred
+     */
     EmailDAO.prototype.encrypt = function(options, callback) {
         this._pgpbuilder.encrypt(options, callback);
     };
@@ -809,6 +929,15 @@ define(function(require) {
     //
 
 
+    /**
+     * This handler should be invoked when navigator.onLine === true. It will try to connect a
+     * given instance of the imap client. If the connection attempt was successful, it will
+     * update the locally available folders with the newly received IMAP folder listing.
+     *
+     * @param {Object} options.imapClient The IMAP client used to receive messages
+     * @param {Object} options.pgpMailer The SMTP client used to send messages
+     * @param {Function} callback [description]
+     */
     EmailDAO.prototype.onConnect = function(options, callback) {
         var self = this;
 
@@ -838,7 +967,11 @@ define(function(require) {
                 // attach sync update handler
                 self._imapClient.onSyncUpdate = self._onSyncUpdate.bind(self);
 
-                // fill the imap mailboxCache
+                // fill the imap mailboxCache with information we have locally available:
+                // - highest locally available moseq
+                // - list of locally available uids
+                // - highest locally available uid
+                // - next expected uid
                 var mailboxCache = {};
                 self._account.folders.forEach(function(folder) {
                     if (folder.messages.length === 0) {
@@ -865,6 +998,7 @@ define(function(require) {
                 });
                 self._imapClient.mailboxCache = mailboxCache;
 
+                // set up the imap client to listen for changes in the inbox
                 var inbox = _.findWhere(self._account.folders, {
                     type: 'Inbox'
                 });
@@ -881,12 +1015,26 @@ define(function(require) {
         });
     };
 
+    /**
+     * This handler should be invoked when navigator.onLine === false. It will discard
+     * the imap client and pgp mailer
+     */
     EmailDAO.prototype.onDisconnect = function() {
         this._account.online = false;
         this._imapClient = undefined;
         this._pgpMailer = undefined;
     };
 
+    /**
+     * The are updates in the IMAP folder of the following type
+     * - 'new': a list of uids that are newly available
+     * - 'deleted': a list of uids that were deleted from IMAP available
+     * - 'messages': a list of messages (uid + flags) that where changes are available
+     *
+     * @param {String} options.type The type of the update
+     * @param {String} options.path The mailbox for which updates are available
+     * @param {Array} options.list Array containing update information. Number (uid) or mail with Object (uid and flags), respectively
+     */
     EmailDAO.prototype._onSyncUpdate = function(options) {
         var self = this;
 
@@ -939,16 +1087,15 @@ define(function(require) {
                     return;
                 }
 
+                // update unread, answered, modseq to the latest info
                 message.answered = changedMsg.flags.indexOf('\\Answered') > -1;
                 message.unread = changedMsg.flags.indexOf('\\Seen') === -1;
-
-                if (!message) {
-                    return;
-                }
+                message.modseq = changedMsg.modseq;
 
                 self.setFlags({
                     folder: folder,
-                    message: message
+                    message: message,
+                    localOnly: true
                 }, self.onError.bind(self));
             });
         }
@@ -963,14 +1110,18 @@ define(function(require) {
 
 
     /**
-     * List the folders in the user's IMAP mailbox.
+     * Updates the folder information from memory (if we're offline), or from imap (if we're online),
+     * and adds/removes folders in account.folders, if we added/removed folder in IMAP. If we have an
+     * uninitialized folder that lacks folder.messages, all the locally available messages are loaded
+     * from memory
+     *
+     * @param {Function} callback Invoked when the folders are up to date
      */
     EmailDAO.prototype._initFolders = function(callback) {
         var self = this,
-            folderDbType = 'folders',
-            folders;
+            folderDbType = 'folders';
 
-        self._account.busy = true;
+        self._account.busy = true; // start the spinner
 
         if (!self._account.online) {
             // fetch list from local cache
@@ -987,15 +1138,13 @@ define(function(require) {
         } else {
             // fetch list from imap server
             self._imapClient.listWellKnownFolders(function(err, wellKnownFolders) {
-                var foldersChanged = false;
-
                 if (err) {
                     done(err);
                     return;
                 }
 
                 // this array is dropped directly into the ui to create the folder list
-                folders = [
+                var folders = [
                     wellKnownFolders.inbox,
                     wellKnownFolders.sent, {
                         type: 'Outbox',
@@ -1005,7 +1154,9 @@ define(function(require) {
                     wellKnownFolders.trash
                 ];
 
-                // are there any new folders?
+                var foldersChanged = false; // indicates if are there any new/removed folders?
+
+                // check for added folders
                 folders.forEach(function(folder) {
                     if (!_.findWhere(self._account.folders, {
                         path: folder.path
@@ -1016,7 +1167,7 @@ define(function(require) {
                     }
                 });
 
-                // have any folders been deleted?
+                // check for deleted folders
                 self._account.folders.forEach(function(folder) {
                     if (!_.findWhere(folders, {
                         path: folder.path
@@ -1027,12 +1178,14 @@ define(function(require) {
                     }
                 });
 
+                // if folder have changed, we need to persist them to disk.
                 if (!foldersChanged) {
                     readMessagesFromDisk();
                     return;
                 }
 
                 // persist encrypted list in device storage
+                // NB! persis the array we received from IMAP! do *not* persist self._account.folders with all the messages...
                 self._devicestorage.storeList([folders], folderDbType, function(err) {
                     if (err) {
                         done(err);
@@ -1045,6 +1198,7 @@ define(function(require) {
             return;
         }
 
+        // fill uninitialized folders with the locally available messages
         function readMessagesFromDisk() {
             if (!self._account.folders || self._account.folders.length === 0) {
                 done();
@@ -1060,7 +1214,7 @@ define(function(require) {
                     return;
                 }
 
-                // sync: messages on disk -> scope
+                // sync messages from disk to the folder model
                 self.refreshFolder({
                     folder: folder
                 }, function(err) {
@@ -1088,7 +1242,12 @@ define(function(require) {
     //
 
     /**
-     * Mark imap messages as un-/read or un-/answered
+     * Mark messages as un-/read or un-/answered on IMAP
+     *
+     * @param {Object} options.folder The folder where to find the message
+     * @param {Number} options.uid The uid for which to change the flags
+     * @param {Number} options.unread Un-/Read flag
+     * @param {Number} options.answered Un-/Answered flag
      */
     EmailDAO.prototype._imapMark = function(options, callback) {
         if (!this._account.online) {
@@ -1103,6 +1262,14 @@ define(function(require) {
         this._imapClient.updateFlags(options, callback);
     };
 
+    /**
+     * If we're in the trash folder or no trash folder is available, this deletes a message from IMAP.
+     * Otherwise, it moves a message to the trash folder.
+     *
+     * @param {Object} options.folder The folder where to find the message
+     * @param {Number} options.uid The uid of the message
+     * @param {Function} callback(error) Callback with an error object in case something went wrong.
+     */
     EmailDAO.prototype._imapDeleteMessage = function(options, callback) {
         if (!this._account.online) {
             callback({
@@ -1126,6 +1293,7 @@ define(function(require) {
             return;
         }
 
+        // move the message to the trash folder
         this._imapClient.moveMessage({
             path: options.folder.path,
             destination: trash.path,
@@ -1134,7 +1302,8 @@ define(function(require) {
     };
 
     /**
-     * Get an email messsage without the body
+     * Get list messsage headers without the body
+     *
      * @param {String} options.folder The folder
      * @param {Number} options.firstUid The lower bound of the uid (inclusive)
      * @param {Number} options.lastUid The upper bound of the uid range (inclusive)
@@ -1192,16 +1361,38 @@ define(function(require) {
     //
 
 
+    /**
+     * List the locally available items form the indexed db stored under "email_[FOLDER PATH]_[MESSAGE UID]" (if a message was provided),
+     * or "email_[FOLDER PATH]", respectively
+     *
+     * @param {Object} options.folder The folder for which to list the content
+     * @param {Object} options.uid A specific uid to look up locally in the folder
+     * @param {Function} callback(error, list) Invoked with the results of the query, or further information, if an error occurred
+     */
     EmailDAO.prototype._localListMessages = function(options, callback) {
         var dbType = 'email_' + options.folder.path + (options.uid ? '_' + options.uid : '');
         this._devicestorage.listItems(dbType, 0, null, callback);
     };
 
+    /**
+     * Stores a bunch of messages to the indexed db. The messages are stored under "email_[FOLDER PATH]_[MESSAGE UID]"
+     *
+     * @param {Object} options.folder The folder for which to list the content
+     * @param {Array} options.messages The messages to store
+     * @param {Function} callback(error, list) Invoked with the results of the query, or further information, if an error occurred
+     */
     EmailDAO.prototype._localStoreMessages = function(options, callback) {
         var dbType = 'email_' + options.folder.path;
         this._devicestorage.storeList(options.emails, dbType, callback);
     };
 
+    /**
+     * Stores a bunch of messages to the indexed db. The messages are stored under "email_[FOLDER PATH]_[MESSAGE UID]"
+     *
+     * @param {Object} options.folder The folder for which to list the content
+     * @param {Array} options.messages The messages to store
+     * @param {Function} callback(error, list) Invoked with the results of the query, or further information, if an error occurred
+     */
     EmailDAO.prototype._localDeleteMessage = function(options, callback) {
         var path = options.folder.path,
             uid = options.uid,
@@ -1225,21 +1416,25 @@ define(function(require) {
     //
     //
 
+    /**
+     * Updates a folder's unread count:
+     * - For the outbox, that's the total number of messages,
+     * - For every other folder, it's the number of unread messages
+     */
     function updateUnreadCount(folder) {
         var allMsgs = folder.messages.length,
             unreadMsgs = _.filter(folder.messages, function(msg) {
                 return msg.unread;
             }).length;
 
-        // for the outbox, the unread count is determined by ALL the messages
-        // whereas for normal folders, only the unread messages matter
         folder.count = folder.path === config.outboxMailboxPath ? allMsgs : unreadMsgs;
     }
 
     /**
      * Helper function that recursively traverses the body parts tree. Looks for bodyParts that match the provided type and aggregates them
-     * @param {[type]} bodyParts The bodyParts array
-     * @param {[type]} type The type to look up
+     *
+     * @param {Array} bodyParts The bodyParts array
+     * @param {String} type The type to look up
      * @param {undefined} result Leave undefined, only used for recursion
      */
     function filterBodyParts(bodyParts, type, result) {
diff --git a/test/new-unit/email-dao-test.js b/test/new-unit/email-dao-test.js
index b0f9857..74c3429 100644
--- a/test/new-unit/email-dao-test.js
+++ b/test/new-unit/email-dao-test.js
@@ -1584,6 +1584,7 @@ define(function(require) {
                     setFlagsStub.withArgs({
                         folder: inboxFolder,
                         message: msgs[0],
+                        localOnly: true
                     }).yieldsAsync();
 
                     dao.onError = function(err) {