Fix CRLF invalid object id bug

[GrahamTheCoder]

When trying to parse a patch file, an InvalidObjectIdException was being thrown because NextLF is used despite not knowing if the file contains CRLFs.

To fix this I've:

• Used the EolCanonicalizingInputStream for patches so they are always CRLF only
• Changed the way newlines are added during patch application to avoid trailing \r when applying to a file containing CRLFs
• Made the ApplyCommandTests and PatchTests run against various combinations of CRLFs and non-CRLFs to ensure we have some coverage of these areas.

[GrahamTheCoder]

Whoops, foiled by Github's UI. I didn't mean to open the PR here - meant it to be here