swh-indexer: Fix configuration to add the tools configuration entry

Without this, the indexer fails on KeyError tools (which blocks further inquiry in swh-search).

I forgot to mention I encountered this when I replied [1]

It's not the same issue as mentioned there (and it's still not blocking for it). It's worth acknowledging there is an issue nonetheless.

It's blocking for swh-search within docker though.

Related to #2854

Test Plan

doco up -f docker-compose.yml -f docker-compose.search.yml up

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Migrated from D4708 (view on Phabricator)