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
%% no merges expected
%% merge of b expected
merging for b
merging b
%%
Contents of b should be "this is file b1"
This is file b1
%% merge expected!
merging for b
merging b
%% merge of b expected
merging for b
merging b