ciall: Add --all to "git add" + remove -a from "git commit"

Newer versions of Git complains about "git add ." when there are deleted
files in the tree:

  warning: You ran 'git add' with neither '-A (--all)' or '--ignore-removal',
  whose behaviour will change in Git 2.0 with respect to paths you removed.
  Paths like 'foo' that are
  removed from your working tree are ignored with this version of Git.

  * 'git add --ignore-removal <pathspec>', which is the current default,
    ignores paths you removed from your working tree.

  * 'git add --all <pathspec>' will let you also record the removals.

  Run 'git status' to check the paths you removed from your working tree.

The addition of --all to "git add" removes that warning, and by removing
-a from "git commit", only deleted files in the current directory and
below will be added to the commit.

1fbe892a-ca24-11e2-8504-001f3b596ec9
tests/perlmodules.t: Add Digest::SHA (libdigest-sha-perl)

I think it's only one program (../sums) that uses Digest::SHA1 now, I'll
remove Digest::SHA1 when I've fixed that somewhen.

7b97703e-ca26-11e2-8854-001f3b596ec9