On Q.2, if being prompted for each file individually doesn't grab you, you could present a screenful of files at a time (perhaps using one of the the columnising codes from 'ls -C' column style to maximise the screen usage), and prefix each with a number. Then prompt the user for a list of numbers (space delimited) of those files to be excluded:

 1)fileA   2)fileB   3)fileC   4)fileD
 5)fileE   6)fileF   7)fileG   8)fileI
exclude? 3 7

 9)fileJ  10)fileK  11)fileL  12)fileM
13)fileM  14)fileN  15)fileO  16)fileP
exclude?
[download]

Depending on the sizes of your directories, filenames and screen you could probably get away with just one prompt in most cases.

You could also allow a first value on the line of I or E (or X) to allow the user to type the shorter list.