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

adding foo
adding bomb
adding a.c
adding dir/a.o
adding dir/b.o
R a.c
R dir/a.o
R dir/b.o
? .hgignore
a.c: unsupported file type (type is fifo)
R a.c