DirCacheCheckout#getContent: also take InputStream supplier

DirCacheCheckout#getContent: also take InputStream supplier

This lets us use DirCacheCheckout for routines that want to write
files in the worktree that aren't available as a git object.

DirCacheCheckout#getContent takes a InputStream supplier rather than
InputStream: if filtering fails with IOException, the data is placed
unfiltered in the checkout. This means that the stream has to be read
again, from the start.

Use it in this way in ApplyCommand. This use is incorrect, though: the
same InputStream is returned twice, so if the read to be retried, the
stream will return 0 bytes. It doesn't really matter, because in
either case, the SHA1 will not match up, and the patch fails.

Change-Id: I2efa9a6da06806ff79b155032fe4b34be8fec09e