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

diff -r 3903775176ed b
--- /dev/null
+++ b/b
@@ -0,0 +1,1 @@
+123
diff -r 3903775176ed b
--- /dev/null
+++ b/b
@@ -0,0 +1,1 @@
+123