OK i just tried and here is what worked :
Create an empty workspace.
Then click on File > Import and select "Existing projects into workspace"
Select the root preenfm3 directory.
Then in "projects" check :
. preenfm3/firmware
. preenfm3/bootloader
. preenfm3/lib
Click finish.
Then Project>build or ctrl B should build everything.
By default (can be changed) the lib is built last, so you have to build everything twice.
Then in "Debug configurations", look at the STM32 config and you'll see:
"Upload and Debug Firmware"
"Upload Release Firmware"
etc....
To use with a STLink board.
To change Debug/Release compilation.
Select all 3 projects "firmware, lib, bootlader" in the project explorer.
Right Click > Build Configurations > Set Active : and choose between Release and Debug.
Then rebuild All.
Don't know if you have a STLink but it works very well (i use a ST Link v2.1 cut from a cheap nucleo 64 boards).
The firmware is uploaded in 5 seconds.
If not, you may need to create dfu flashable objects.
So have a look in
. preenfm3/script/create_object.sh
Let me know if you have any questions