Make "stg refresh" subdirectory safe

Make "stg refresh" subdirectory safe

Make "stg refresh" subdirectory safe by letting it internally cd up to
the top of the worktree. This is possibly not the best long-term fix;
one could argue that the refresh subroutine should instead be safe to
run from a subdirectory. However, refreshing from a subdirectory
currently only refreshes changes that are in the index, and not
changes in the working directory, and that has to be fixed.

Signed-off-by: Karl Hasselström <kha@treskal.com>