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cyprjmgr have a couple of flags that might help you:
-prj Specifies the target project on which all the command line
options will be targeted. In case target project is not
specified, Top Project of the workspace becomes the target
-p Sets the Top Project in the workspace
I haven't test it yet, so maybe you can do a dummy workspace with two projects in it and test it. Here i placed the flags of some tools used by PSoC Creator (including cyprjmgr) http://uciee47.blogspot.mx/2017/01/psoc-creator-tools.html
Let me know if it helps :D
I have three projects, I want to build them in a certain order.
How can I select the compilation order of each one, from 1 to 3 by command line?