shell: support for multiple GUI (non-batch) commands, move GUI refresh from wrc_main to the shell code

- CRITICAL: initialize Fine Pulse Generator prior to DDS (see comments in the code)
- temporarily disable gain scheduling in SoftPLL to speed up locking during development
- migrate printfs() to debug calls

dev/spi_flash: fixed incorrect read/write address (regression added while adding support for 4-byte address mode)