Fix the broken/missing tocs in all the modules

We need to review all the TOCs in the doc, because most of them are broken.

• We should remove :orphan: blocks, pages should always be referenced in a TOC. When a page is marked as :orphan:, accessing it will not show its position in the navigation hierarchy.

• We should remove "manual" TOCs using :ref:, as those don't count for the global TOC. All the TOCs should be put in a ".. toctree::" block, using :caption: if needed to present it properly in a separate section.

• Each page should always have one title as the top-level header.

Here is the list of modules that need to be reviewed and the associated diffs:

• swh.core (ardumont)
• swh.dataset (seirl)
• swh.deposit (ardumont)
• swh.graph (seirl) -> swh-graph!42 (closed)
• swh.indexer (ardumont)
• swh.journal
• swh.lister (ardumont) -> swh-lister!330 (closed)
• swh.loader
• swh.model (seirl) -> swh-model!53 (closed)
• swh.objstorage
• swh.scheduler
• swh.storage
• swh.vault
• swh.web

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Migrated from T1984 (view on Phabricator)