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Hi Pavel Yermolenko,
Yes, the mesh app note is based on ModusToolbox 1.1. I hope you are using ModusToolbox2.0.
I will contact cypress technical document team and inform this. We will take necessary steps to updated the appnote ASAP.
Thank you for sharing this issue with us.
'Application settings' can be changed by editing the makefile in MTB 2.0. There is no GUI for it.
Please go through Migrating from ModusToolbox v1.1 to v2.x - KBA229043
Please go through C:\Users\username\ModusToolbox\ide_2.0\docs\doc_landing.html for IDE based documentation.