Some issues sent in by Mauno in http://moodle.org/mod/forum/discuss.php?d=99001#p438263 (this is not an exact copy of the message), see thread for details.
1) First round of checking the code in HEAD done and I am ready to sink into the ground - now also editor theme standard is gone so in practice there is nothing left of my several weeks of testing. Most of the default configuration I had done was in that theme to avoid overwriting previous files in upgrading, to keep tinymce doing the same things as htmlarea and to be able to add extra features to moodle without modifying the code of tinymce itself. The main idea in TinyMCE themes is that theme (usually advanced) has all default settings in file editor_template.js and external configuration is used only if necessary. If we use only advanced theme we are tied to functions there - I thought we needed to create a "moodle specific editor theme" - standard - that can be modified to look like moodle and not to use the prototype advanced theme of Moxiecode. Basic code of theme standard is exactly the same code as in theme advanced - you just need to use word standard in init code instead of advanced. Skins can be used for setting colors, fonts etc css but themes are a larger set of code in tinymce.
2) contextmenu should be used with advanced theme and standardmenu (modified settings for shortcut keys/accessibility and right mouse click menus) only with standard theme that does not exist anymore.
3) There's also some confusion in init code: Imagemanager,filemanager vs moodleimage and moodlelink by Glen, still course files are not used at all. Have you done a new filemanager plugin, Mathieu?
4) xhtml_ruleset.txt - we should be able to select if we want to use it or not because media plugin does not allow embedding media with full xhtml rule set
5) Role based settings - for example students should probably not have media button but teachers need access to course files - the reason why I used separate init code for students and teachers - selection of code can be made with capability checking. Without these file/imagemanager (moodleimage), links (moodlelink), anchors and embedding media are "torso". Teachers need the correct button (plugin that gives access to course files) to be able to add course files inside content.