Only apply exclusion rules when available

[jason0x43]

A recent change to the exclusion logic causes all files to be excluded by default (files are only added to the input list if an exclude rule is provided and it doesn't match). This PR causes files to be added to the input list if there is no exclude rule or if the provided exclude rule doesn't match a file.

[aciccarello]

Thanks! Could you also add a unit test to make sure that this error doesn't happen again?

[jason0x43]

Will do

[aciccarello]

This should fix #421

[jason0x43]

I updated the unit tests to check that the exclusion rules are applied properly to both directory and file entries. The reason the tests were passing the after the initial update is that exclusion was handled different if entries in the input list were directories vs files, and the tests were only trying directories.

[jason0x43]

I'm not entirely sure that this will deal with #421. At least, the issue I was experiencing is that 0.5.6 wasn't pulling in any files (vs #421 saying that extra files were being pulled in) because all individual input files were being excluded if no exclude rule was provided.