cmake: Ninja: ld: Use the correct depfile in the second pass

When building for Ninja we were accidentally using the wrong depfile
in the second pass. This commit moves the LINKER_SCRIPT_DEP logic into
the custom command function so that it can be linker-pass-aware and
set the depfile appropriately.

This should fix an issue where Ninja reported:

ninja: error: expected depfile 'zephyr/linker.cmd.dep' to mention
'zephyr/linker_pass2.cmd', got 'zephyr/linker.cmd'

But this has not been reproduced. It has however been confirmed that a
dependency issue with linker_pass2.cmd has been fixed because ninja no
longer regenerates linker_pass2.cmd on every build like this:

$ ninja
[1/79] Generating always_rebuild
Building for board qemu_x86
[2/3] Generating linker_pass2.cmd
[3/3] Linking C executable zephyr/zephyr.elf

Now:

$ ninja
[1/78] Generating always_rebuild
Building for board qemu_x86

Signed-off-by: Sebastian Bøe <sebastian.boe@nordicsemi.no>