We had the embed switch the other way round in previous versions of Amethyst. We will switch it back again.
Th embed business is peculiar. FB seems to 'fix up' these embeds on the fly, but the syntax is actually incorrect, as has been pointed out many times by people who try to do batch builds instead of using FB to do it. Adobe at one time promised to address this problem (the inconsistency between the command line compiler and the way FB handles Embed), but since they lost interest in FB and Flex, I suspect this isn't likely.
I don't recall if there was such an option, but maybe make the "/" to embeds a command, like in edit menu or such. But given the extra details you provided, I can see how this can be a gray area.
I'd like to mention another possible issue, but that's probably because we have our setup done in a weird kind of way.
Our project structure is something like this:
/flaProjects - contains CS5 projects to make our external/embedded swfs
/libs - Our flaProjects's swc files for embedded swfs
/sdks - Currently we have flex 3.6A sdk in there, this allows a new employee to be ready without having to download anything special, and also makes sure we all use the same one.
/src - our sources, things to compile etc
/utils - things like TheMiner swf which allows to profile or something like that
So what I've realized is that when I load the solution, all files are parsed for auto-complete functionality, but it doesn't parse only under /src but all folders under root. I'm not sure if that is ever desirable since all refs should already be in the references section and source files should be under /src. but, what if we could exclude those root folders from IntelliSense parsing by having a "exclude from IntelliSense parsing", this could translate into an extra attribute or custom attribute of the folder entry in the amproj file like:
<Folder Include="flaProjects" ParseIntelliSense="False" />
Here's an example of what I get in my IntelliSense parsing errors output:
Background parse of 'D:\Src\Flash\UIMain\AllianceWarfare\sdks\3.6.0\frameworks\projects\airframework\src\mx\controls\FlexNativeMenu.as' requeued
Hoping I'm not too much of a pest with all these comments/suggestions.