make all commands be repo-wide by default
- refactor code in commands.py so that:
if no pattern is given, the command will be repo-wide
else it will work on the working dir
- update the doc
- fix the tests
*** 'a\nc\n\n\n\n' 'a\nb\n\n\n'
*** 'a\nb\nc\n' 'a\nc\n'
*** '' ''
*** 'a\nb\nc' 'a\nb\nc'
*** 'a\nb\nc\nd\n' 'a\nd\n'
*** 'a\nb\nc\nd\n' 'a\nc\ne\n'
*** 'a\nb\nc\n' 'a\nc\n'
*** 'a\n' 'c\na\nb\n'
*** 'a\n' ''
*** 'a\n' 'b\nc\n'
*** 'a\n' 'c\na\n'
*** '' 'adjfkjdjksdhfksj'
*** '' 'ab'
*** '' 'abc'
*** 'a' 'a'
*** 'ab' 'ab'
*** 'abc' 'abc'
*** 'a\n' 'a\n'
*** 'a\nb' 'a\nb'
done