docs: sort the top-level directories into five sections by what the reader wants
Every docs directory moves under 1-getting-started, 2-handbook, 4-implementation or 5-project; the options reference (section 3) comes from the website and has no directory here. trust-boundary stays whole under the handbook for now. web-ui, swarm and tools split between handbook and implementation, and the command-line references move to 2-handbook/reference. Links, path references in code and nix, and the docs index follow the moves; no page content changes.
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//!
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//! **The internal one** — [`agent_token`] — is the agent's own `main` account on
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//! the swarm's homeserver, minted with the swarm's appservice token and stored
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//! where the agent's daemon reads it. See docs/swarm/credentials-reference.md for why
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//! where the agent's daemon reads it. See docs/2-handbook/swarm/credentials-reference.md for why
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//! `main` is the one name [`put_matrix_account`] refuses to write.
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//! [`hive_sender`] mints each **hive's** sender account the same way, sharing this module's helpers with [`agent_token`].
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//! [`operator_admin`] makes authelia's operators homeserver admins with the same
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