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emFile is still not available in ModusToolbox 2.0 (MTB). However, we have the SD Host Controller driver in MTB which provides the user an easy method for accessing standard Host Controller Interface (HCI) registers and provides some simple functionality on top of the HCI for reading and writing data to an SD card, eMMc card or a SDIO device.
You can make use of this. FreeRTOS is available as a pre-built library. ModusToolbox doesn't use a component based schematic design like PSoC Creator. You need to make use of the device configurator to enable the required peripherals which will eventually generate files which can be used in firmware.
Also, the migration may not be straightforward since the PSoC6 uses Peripheral Driver Library (PDL) APIs than the component APIs you use on PSoC5.
I recommend undertstanding all about PSoC6 development in MTB and then beginning the migration. You can find the code examples here: GitHub - cypresssemiconductorco/Code-Examples-for-ModusToolbox-Software