docs: note gen-docs pruning of deprecated command pages

Brendan Lynchrequested to merge
bl-agents-gen-docs-prune-note into main

Description

Follow-up documentation to !3515 (merged) (resolves #8341 (closed)), which made make gen-docs prune generated pages.

Updates the Updating a command's docs entry in AGENTS.md to note that make gen-docs now prunes pages for removed, deprecated, and hidden commands (and deletes any emptied directories). Agents should regenerate and commit the deletions rather than hand-deleting files under docs/source/.

CLAUDE.md inherits this through @AGENTS.md, so no separate change is needed. Only agent-facing instructions change — no Go source is touched, so generated docs are unaffected.

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