Switch include/exclude filters to arrays and use minimatch directly

I wanted to use glob statements like this: `**/public/img/**/*.*`, `**/public/{js,css}/app/*.{js,css}` but the existing filter handling would split the second filter at the commas and would also not use minimatch because of the asterisks. I changed the implementation to take an array of filters: `--include="filterA" --include="filterB"`, rather than splitting on commas, and to use minimatch directly rather than handling asterisks differently.

Let me know if my implementation misses any desired behavior.