To get a .NET application from your development environment to an ARM Linux device like the ComfilePi, you need to perform the following steps in order:
ssh {comfilepi_user}@{comfilepi_ip_address} chmod +x {comfilepi_folder}/{executable_file}
With the binary files successfully deployed to the target device and the main binary marked as executable, you can run the application by simply invoking the main binary executable from a terminal.
./{executable_file}
If you are invoking the application from an SSH session, and the application requires and X11 display, you must first set the DISPLAY environment variable to the local display, then run the executable file.
export DISPLAY=":0.0"
./{exectuable_file}