The trunk is currently setup as a Flex Library Project. When you check it out, in theory it should compile all classes into a SWC.
Currently the flexLibProperties file needs to be updated to reflect new classes being added and removed. To do this, checkout trunk as a Flex Library Project, right-click on the project in the Navigator, select Properties, go to Flex Library Build Path and in the Classes tab uncheck the very top box next to src and then recheck it. This will select all classes in the library so that the project can properly compile to a SWC.
After adding or removing new files into the library, verify that all classes are selected and then commit your changes (including the flexLibProperties file).
Also, to prevent future Flex class additions into the library, in the Library path tab (next to the Classes tab above) open up the Flex SDK and remove all SWCs except for the following:
These are the same SWCs that are in an ActionScript Project. All other SWCs are only used in Flex projects and not needed for an AS-only project or library.
Note: Base64Encoder and Base64Decoder will no longer work once you remove the other SWCs since those classes are in the mx directory.