We are using CY8CKIT-059 for prototyping. Kit is connected to a mini PC with Fedora on it and I want to update the kit firmware over this mini PC via SSH. To do so, I need a tool to upload the hex file over the console such as avrdude used for Arduino. How can I achieve this?
You need to have a bootloader on the PSoC. Probably your connection to the min-PC is a serial port, so you need a UART bootloader. AN68272 describes one and gives you source code for it (though not for Linux) which you can use. There is also AN73503 for a USB HID bootloader (and it seems to have the actual bootloader host as library which should be easy to port).