You'll also want to clear the application cache and restart PHP-FPM, just to be sure. If you're running your AtoM by following our default Ubuntu 14.04 installation instructions, you can enter:
RE: HTML in the static pages
As I understand it, there are some helper functions built into the page to assist people just entering raw text, who don't know HTML - so adding a couple line breaks will be interpreted as a <br/> element on save. Can you try just not using line breaks, and instead using the HTML to control the layout? It makes your HTML less readable at a glance but as far as I'm aware this should stop the additional elements from being added and solve your issue. I haven't tested it yet though. Let us know how it goes.
RE: Deleting the Manage menu
This is interesting and I've never tried this before, but I'm not surprised. I'm glad you managed to recover your site. There are some elements in AtoM that have been coded as if every single element is customizable via the user interface, but in reality there are some exceptions that will break the functionality - it looks like you've discovered one of them. In 2.3 there is an option to hide the Language menu in Admin > Settings > Default page elements, but my guess is that removing any of the main menus entirely will break AtoM - the one exception might be the QuickLinks menu. It would be great to improve this, but it would require investigation, analysis, and development. For now, if you don't want your users acessing those menus, remove some of the nodes and control access via the Permissions module and Users/Groups.
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