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Now, after the first start of the generator, a file is created:

riocore/toolchains.json

there you can enter the paths to your toolchains, these are then transferred to the makefile.

under windows please note that backslashes must be double

 

so you do not need to add the toolchains to your enviroment variables
 

Now i am quickly getting out of my depth, It looks like you maybe missing the link to the XML file in your hal? as you are not showing the EK1100 in the list of Pins.

do you have something similar to
loadusr -W lcec_conf ethercat-conf.xml

You also seem to be missing the Readall / writeall for lcec can you post your hal?

In your xml? and when you start from the cmdline are you getting any errors?