Set +x in index in same-rename-different-mode baseline

Since #1618, which introduced `gix-merge::merge tree::run_baseline`
and the functionality it tests, that test has failed on Windows
when run with `GIX_TEST_IGNORE_ARCHIVES=1`. This happens because,
while `chmod +x` commands run and exit indicating success in MSYS
environments such as Git Bash, they do not actually make a change.

Multiple cases (all sub-cases of the same faililing test) would
fail this way. But the test fails fast, so only one is reported.
The first to fail this way is `same-rename-different-mode`, which
shows:

    --- STDERR:              gix-merge::merge tree::run_baseline ---
    failed to extract 'tests\fixtures\generated-archives\tree-baseline.tar': Ignoring archive at 'tests\fixtures\generated-archives\tree-baseline.tar' as GIX_TEST_IGNORE_ARCHIVES is set.
    thread 'tree::run_baseline' panicked at gix-merge\tests\merge\tree\mod.rs:83:21:
    assertion `left != right` failed: same-rename-different-mode-A-B-reversed: Git caught up - adjust expectation Git works for the A/B case, but for B/A it forgets to set the executable bit
      left: Sha1(d75339daa64f3a1d98947623eee7bbb218e6c87d)
     right: Sha1(d75339daa64f3a1d98947623eee7bbb218e6c87d)

This commit fixes that by using `git update-index --chmod=+x` to
stage the intended effect of `chmod +x`. The `chmod +x` commands
are still run, to avoid non-intended and potentially bug-prone or
confusing differences between the metadata on disk and what is
staged and commited, on systems where Unix-style permissions are
supported on disk and `chmod +x` modifies them.

Although only one of the two approaches is needed on any particular
system in these tests, deciding based on the operating system is
more complicated. It would also be misleading, because the effect
of the two kinds of commands is not, in *general*, the same: one
operates on files in the working tree, and the other operates on
the index. Therefore, both are used, for simplicity and clarity.

For readability, adjacent `chmod +x` commands are also combined
into one. This way, each place that has both `chmod +x` logic and
`git update-index --chmod=+x` logic can have a single command for
each, that clearly relate to each other.

As noted above, the change in this commit is not sufficient to fix
that failing test, because a subsequent assertion still fails. This
will be detailed and fixed in a subsequent commit. (This commit
also does not yet update generated archives.)

gix-merge/tests/fixtures/tree-baseline.sh

@@ -475,8 +475,8 @@ git init same-rename-different-mode
 
   git checkout A
   write_lines 1 2 3 4 5 >a/x.f
-  chmod +x a/x.f
-  chmod +x a/w
+  chmod +x a/x.f a/w
+  git update-index --chmod=+x a/x.f a/w
   git mv a a-renamed
   git commit -am "changed all content, add +x, renamed a -> a-renamed"
 
@@ -486,8 +486,8 @@ git init same-rename-different-mode
   git commit -am "changed all content, renamed a -> a-renamed"
 
   git checkout expected
-  chmod +x a/x.f
-  chmod +x a/w
+  chmod +x a/x.f a/w
+  git update-index --chmod=+x a/x.f a/w
   write_lines 1 2 3 4 5 6 >a/x.f
   git mv a a-renamed
   git commit -am "Git, when branches are reversed, doesn't keep the +x flag on a/w so we specify our own expectation"