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doc: Explicitly mark roles dirty in tutorial (WIP)

TUF does not reliably mark roles as dirty whose metadata needs
to be re-generated.

Only roles that have changed are marked as dirty, but sometimes
roles metadata needs to be updated, although the role wasn't
changed directly (see #958).

Furthermore, the tutorial assumes at one point that the reader
leaves and re-enter the interpreter session, being forced to reload the
signing keys, roles that later need to be re-written, are marked as
dirty. If the reader does not leave the interpreter, the roles are
not marked as dirty (see #XXX).

To not confuse the reader with flawed state-keeping, and to never
write an inconsistent repository to disk, the tutorial lets the
reader explicitly mark all roles that need to be re-written as
"dirty".

This can be changed once above issues are fixed.

TODO: Create issue #XXX and replace in tutorial snippet comments
and in this commit message

Signed-off-by: Lukas Puehringer <lukas.puehringer@nyu.edu>

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