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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//! Trade-off (accepted — issue tracker "perms borked"): a misbehaving harness
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//! could skip its own cleanup, which the host-side version was meant to
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//! prevent. But a compromised harness is already inside the container trust
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//! boundary (`docs/trust-boundary/security.md`), and these are ephemeral local artifacts — so
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//! boundary (`docs/2-handbook/trust-boundary/security.md`), and these are ephemeral local artifacts — so
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//! the honest fix is to clean them up where they live.
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use std::path::Path;
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