You can create a custom goal. There is a specific “Make a goal” view where you can view / add / edit them. We use them in our project to create individual components of our project. The trick is that you will need to create a new target for each subdirectory. The bonus is that you easily copy each target into subdirectories.
Also, to save time, you need to know the short cuts by heart: (in Indigo) F9 to restart the last target and CTRL + SHIFT-Q, M to display the Make Target view .; -)
In addition, you should upgrade to Indigo - if your plugins allow this. The cdt plugin has improved significantly since then.
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