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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@ -84,7 +84,7 @@ pub struct InboxRow {
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}
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/// One delivered message in a `Recv` response.
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/// See `docs/process/conventions.md::Broker delivery + ack cycle` for the
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/// See `docs/5-project/process/conventions.md::Broker delivery + ack cycle` for the
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/// full delivery/ack/requeue story.
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#[derive(Debug, Clone, Serialize, Deserialize)]
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pub struct DeliveredMessage {
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@ -130,7 +130,7 @@ pub struct ReminderStats {
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/// thread kinds can land without breaking existing handlers.
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/// Per-flavour scoping + per-variant fields + clock-anomaly
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/// saturation behaviour live in
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/// `docs/process/conventions.md::Loose-ends wire shape`.
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/// `docs/5-project/process/conventions.md::Loose-ends wire shape`.
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#[derive(Debug, Clone, Serialize, Deserialize)]
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#[serde(tag = "kind", rename_all = "snake_case")]
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pub enum LooseEnd {
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@ -73,7 +73,7 @@ pub fn builtin_tools_for(perms: &[Permission]) -> Vec<&'static str> {
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/// `Execution` already grants shell execution to the parent agent, via the
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/// out-of-process `bash` MCP server (`mcp__bash__run`/`status`/`kill` —
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/// see the variant's own doc comment). A subagent has no MCP server at all
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/// by default (`docs/tools/subagent.md`), so there is no `mcp__bash__*` for
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/// by default (`docs/2-handbook/tools/subagent.md`), so there is no `mcp__bash__*` for
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/// it to inherit that permission through; it gets Claude's own `Bash`
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/// instead.
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///
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