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## API Overview
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- `thread/start` — create a new thread; emits `thread/started` (including the current `thread.status`) and auto-subscribes you to turn/item events for that thread. When the request includes a `cwd` and the resolved sandbox is `workspace-write` or full access, app-server also marks that project as trusted in the user `config.toml`. Pass `sessionStartSource: "clear"` when starting a replacement thread after clearing the current session so `SessionStart` hooks receive `source: "clear"` instead of the default `"startup"`. Experimental `runtimeWorkspaceRoots` replaces the thread-scoped runtime workspace roots used to materialize `:workspace_roots`; paths must be absolute. For permissions, prefer experimental `permissions` profile selection by id; the legacy `sandbox` shorthand is still accepted but cannot be combined with `permissions`. Deprecated experimental `multiAgentMode` is ignored; use Ultra reasoning effort for proactive multi-agent behavior. Experimental `environments` selects the sticky execution environments for turns on the thread; omit it to use the server default, pass `[]` to disable environments, or pass explicit environment ids with per-environment `cwd`. Experimental `selectedCapabilityRoots` selects environment-owned plugin or standalone-skill roots using environment-native absolute paths. Skills found below those roots are listed and read through the owning environment. Stdio MCP servers declared by selected plugins are also started in that environment; HTTP MCP declarations remain inactive.
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- `thread/start` — create a new thread; emits `thread/started` (including the current `thread.status`) and auto-subscribes you to turn/item events for that thread. When the request includes a `cwd` and the resolved sandbox is `workspace-write` or full access, app-server also marks that project as trusted in the user `config.toml`. Pass `sessionStartSource: "clear"` when starting a replacement thread after clearing the current session so `SessionStart` hooks receive `source: "clear"` instead of the default `"startup"`. Experimental `allowProviderModelFallback` lets providers backed by an authoritative static model catalog replace an unavailable requested `model` with the catalog default; dynamic or cached catalogs preserve the requested model. Experimental `runtimeWorkspaceRoots` replaces the thread-scoped runtime workspace roots used to materialize `:workspace_roots`; paths must be absolute. For permissions, prefer experimental `permissions` profile selection by id; the legacy `sandbox` shorthand is still accepted but cannot be combined with `permissions`. Deprecated experimental `multiAgentMode` is ignored; use Ultra reasoning effort for proactive multi-agent behavior. Experimental `environments` selects the sticky execution environments for turns on the thread; omit it to use the server default, pass `[]` to disable environments, or pass explicit environment ids with per-environment `cwd`. Experimental `selectedCapabilityRoots` selects environment-owned plugin or standalone-skill roots using environment-native absolute paths. Skills found below those roots are listed and read through the owning environment. Stdio MCP servers declared by selected plugins are also started in that environment; HTTP MCP declarations remain inactive.
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-`thread/resume` — reopen an existing thread by id so subsequent `turn/start` calls append to it. Accepts the same permission override rules as `thread/start`.
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-`thread/fork` — fork an existing thread into a new thread id by copying the stored history; if the source thread is currently mid-turn, the fork records the same interruption marker as `turn/interrupt` instead of inheriting an unmarked partial turn suffix. The returned `thread.forkedFromId` points at the source thread when known. Accepts `ephemeral: true` for an in-memory temporary fork, emits `thread/started` (including the current `thread.status`), and auto-subscribes you to turn/item events for the new thread. Experimental clients can pass `excludeTurns: true` when they plan to page fork history via `thread/turns/list` instead of receiving the full turn array immediately. Accepts the same permission override rules as `thread/start`.
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-`thread/start`, `thread/resume`, and `thread/fork` responses include the legacy `sandbox` compatibility projection. `instructionSources` lists loaded instruction files using each source environment's native absolute path syntax, including files loaded from remote environments. Experimental clients can read `runtimeWorkspaceRoots` for the thread-scoped runtime roots and `activePermissionProfile` for the named or implicit built-in profile identity/provenance when known. Their deprecated experimental `multiAgentMode` field, and the corresponding thread setting, always report `explicitRequestOnly`; Ultra reasoning effort is the source of proactive multi-agent behavior.
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