Make singularity-wrapper more portable

[kjsanger]

This replaces use of bash in the wrapper generator that is hosted inside the container, making it usable in containers that do not have bash installed e.g. Alpine Linux.

It also removes a dependency on jq, again for portability. This requires a change the manifest of executables from JSON to a flat list.

[dkj]

Don't know how important these are. Shellcheck reports:

Line 79:
    local dir="$1"
    ^-- SC3043 (warning): In POSIX sh, 'local' is undefined.
 
Line 80:
    local exe="$2"
    ^-- SC3043 (warning): In POSIX sh, 'local' is undefined.
 
Line 84:
        echo -e "\nERROR:\n  A Docker image name is required"
             ^-- SC3037 (warning): In POSIX sh, echo flags are undefined.
 
Line 110:
    local dir="$PREFIX/bin"
    ^-- SC3043 (warning): In POSIX sh, 'local' is undefined.
 
Line 164:
            echo -e "\nERROR:\n  Invalid option"
                 ^-- SC3037 (warning): In POSIX sh, echo flags are undefined.
 
Line 173:
    echo -e "\nERROR:\n  The manifest of executables at '$MANIFEST_PATH' does not exist"
         ^-- SC3037 (warning): In POSIX sh, echo flags are undefined.
 
Line 177:
operation="$@"
          ^-- SC2124 (warning): Assigning an array to a string! Assign as array, or use * instead of @ to concatenate.
 
Line 180:
    echo -e "\nERROR:\n  An operation argument is required"
         ^-- SC3037 (warning): In POSIX sh, echo flags are undefined.
 
Line 194:
        echo -e "\nERROR:\n  Invalid wrapper operation '$operation'"
             ^-- SC3037 (warning): In POSIX sh, echo flags are undefined.

(Assign as array was already there).

Are the local and echo -e significant?

[kjsanger]

Are the local and echo -e significant?

They are supported by dash, which is the default shell for alpine and busybox, which are the main alternatives to Debian/Redhat (and derivatives) that we're likely to see.

The array assignment is wrong (but accidentally give the correct result here, as it turns out). It should be just operation="$1" because the script arguments have been shifted relative to OPTIND a few lines previously. I will fix that.