In order to create a SWC using FlashDevelop you can use the ExportSWC plugin.
This makes the process really simple.
I was wondering how I could create a SWC like the one available in the AS3 Core Lib for example.
You need to have FlashDevelop and the Flex SDK.
At the time of this writing the current version of FlashDevelop is 3.2.1, of ExportSWC is 1.2.3803.31343 and of the Flex SDK is 4.1.
If you need instructions on how to configure FlashDevelop with the Flex SDK, here you have the info you need. Although it’s for an older version of the Flex SDK, the steps are all the same.
In order to install the plugin, just download and double click it. Follow the steps and that’s it.
The next time you open FlashDevelop you’ll see a new button in the toolbar.

Create a new project:
Project->New Project->AS3 Project
Choose a name for the project, set the Location and define a package.

You’ll end up with this:

If you click the SWC/MXI button in the toolbar, the new SWC will appear in the “bin” folder.

This is it.
In this case, you only have the Main.as Class in the src/com/mydomain/test/ folder, which is created automatically, but you can have all the Classes you want.
Just make sure you have all the Classes that are required for the compilation. At a certain time I didn’t, and The SWC file wasn’t being created. it just failed silently.