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?
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.
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"Efficiency is intelligent laziness." -David Dunham
"Think for yourself!" - Abigail
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