handle comutations in subdirs of the git repository

handle comutations in subdirs of the git repository

Eg, a computation might be run in "foo/" and refer to "../bar" as an
input or output.

So, the subdir is part of the computation state.

Also, prevent input or output of files that are outside the git
repository. Of course, the program can access any file on disk if it
wants to; this is just a guard against mistakes. And it may also be
useful if the program comunicates with something less trusted than it,
eg a container image, so input/output files communicated by that are not
the source of security problems.