The MachXO2 device family supports dual function pins to provide more general purpose IOs for applications that require high pin counts. The sysConfig and JTAG pins of the device are all dual function pins for the MachXO2 family. These pins can be used as dedicated configuration / programming pins, or as general purpose IO pins. The behavior of these pins can be different in configuration mode and user mode. The definition of configuration mode and user mode can be found in TN1204, MachXO2 Programming and Configuration Usage Guide.
During configuration mode, one or more sysConfig / JTAG ports can be reserved for device configuration / programming purpose. The output pins of a reserved sysConfig / JTAG ports are tri-stated during configuration mode. They will not drive out signals until the port receives a command to start the configuration / programming process. The Pin Function and Pin Direction columns of the tables under Programming and Configuration Pins section of the TN1204 explain the default behavior of sysConfig and JTAG pins during the configuration mode.
The pins included in a particular sysConfig port can also be preserved or remain live after the device is programmed and in user mode. This is governed by several PERSISTENT fuses that the user can optionally set in the design. However if specific PERSISTENT fuses are not set, the user can utilize these dual-purpose sysConfig pins for their own customized design. The pins will be defaulted as unused pins if neither a PERSISTENT mode is set nor an user function is not implemented. This will set the unused I/O to include a pull down and output tristate.