support/graph-depends: make sure mandatory deps are displayed

support/graph-depends: make sure mandatory deps are displayed

The current graph-depends implementation filters out a number of
"mandatory" dependencies that all packages have: dependency on
"toolchain" and dependency on "skeleton".

Despite this filtering, in full graph dependencies, "toolchain" and
"skeleton" are still shown, because they are target packages, and
therefore appear in the result of "make show-targets". Thanks to this,
they will be visible as dependencies of the "ALL" node, which is the
root of the dependency tree.

However, as we are going to introduce host-skeleton as a "mandatory
dependency" to be filtered out, this is no longer going to work.

This commit adjusts the remove_extra_deps() function to ensure that
when a mandatory dependency is removed, this dependency exists between
the root of the dependency tree and the mandatory dependency.

This issue was noticed by Yann E. Morin, and this commit provides a
different implementation than what Yann proposed in
https://patchwork.ozlabs.org/patch/910453/.

Signed-off-by: Thomas Petazzoni <thomas.petazzoni@bootlin.com>
[yann.morin.1998@free.fr:
  - list mandatory deps before removing them
  - fix flake8 warnings
]
Signed-off-by: "Yann E. MORIN" <yann.morin.1998@free.fr>
Signed-off-by: Thomas Petazzoni <thomas.petazzoni@bootlin.com>