fix generating a list of files/directories ignored by git

"git ls-files --others --ignore --exclude-standard --directory" doesn't
include the files that for example get ignored by this .gitignore line:
-----
default/*
-----

Without the "--directory" line it includes these files, but doesn't include:
-----
folder/
-----

So combine those 2 commands. The next line (grep -xFvf) requires an exact
match (-x). As a result the files in the 1st example were included in the
.etckeeper file.

Reference: http://stackoverflow.com/questions/466764/show-ignored-files-in-git#answer-1446609
Fix handling of git ignores like dir/* Thanks, Pim van den Berg
rename file, since it is a markdown file

Hmm