Update manifest to exclude swh/provenance/tools

This is tooling around swh-provenance and not provenance itself but, it's:

• not covered

• not declaring its dependencies in the main setup.py

• missing init.py from that folder onward

• failing the main build [1]

• [1] https://jenkins.softwareheritage.org/view/swh%20master%20(draft)/job/DPROV/job/tests/706/console

Related to swh/infra/sysadm-environment#4230 (closed) (probably)

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Migrated from D7900 (view on Phabricator)