Concerning your response issue, it’s because you need to specify the port of the target where you want the response to be sent. There are macros to support this (adl_atSendRspPort AFAIR…). You can get the port identifier from which the command has been received in the adl_atCmdPreParser_t structure.
For the WIP issue, you should ask in the dedicated forum thread…
It’s true that using run configurations is convenient to build + download in one click.
A workaround can be to enable the automated build when you save a file (Project properties > C/C++ Build > Behavior > Build on resources save). It’s not perfect (trends to trigger the build several times for a single file save…) but it can make you sure that what you download (out of the Run Configuration) is always up to date…
We still have to take some time to try reproducing the troubles you have with the Run Configuration, in order to find another workaround if possible.
Can you just remind me if you’re getting troubles also with a simple Hello World app?