Hello,
you can use some Windows commands or functions to run through the folders. It really depends on the names of the folders. For example, when you are processing individual frames and the folders are named Frame0001 - Frame1000 you can use for loop to run through them. Simple example:
set StartFrameNumber=1
set StopFrameNumber=1000
set MyPath=D:\Data
for /l %%F in (%StartFrameNumber%, 1, %StopFrameNumber%) do (
RealityCapture.exe -addFolder %MyPath%%%F
)
For renaming the folders and files, you can use for example multi rename tool in Total Commander.